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Study identifies functional roles of individuals within microbial consortium for breaking down switchgrass for biofuel production

Each contig (overlapping segment of DNA derived from shotgun sequencing) was plotted against its average read coverage per base (X axis), and its GC% (guanine-cytosine) content (Y axis). The surface area of each circle is proportional to the length of the contigs in bp, giving an intuitive visualization of how much metagenomic sequence is covered by each cluster. Phylogenetic bins are represented by different colors, while grey circles represent (typically smaller) contigs that were not assigned to a bin. Source: D’haeseleer et al. Click to enlarge.

Working with a compost-derived consortium of thermophillic bacterium adapted to grow on switchgrass, and using a combination of metagenomic and metaproteomic technologies, a collaboration led by researchers with the US Department of Energy’s (DOE’s) Joint BioEnergy Institute (JBEI) has identified individual microbial species whose enzymes were the most active in deconstructing the switchgrass biomass.

The study marks the first time that the functional roles of individual microbial populations within a consortium have been linked with specific enzyme activities—in this case cellulase and hemicellulase—said Steven Singer, director of JBEI’s microbial communities program. “Since these activities are broadly relevant to biofuel production, this is one of the first real-world applications being met by combining metagenomics and metaproteomics,” Singer said.

Major institutes in addition to JBEI participating in this collaboration included DOE’s Joint Genome Institute (JGI), and EMSL, the Environmental Molecular Sciences Laboratory, a national scientific user facility at Pacific Northwest National Laboratory (PNNL). An open-access paper on the research is published in the journal PLOS One.

Unlike the simple sugars in corn grain, the cellulose and hemicellulose in biomass are difficult to extract in part because they are embedded in a tough woody material called lignin. Thermophilic microbes—microbes that thrive at extremely high temperatures and alkaline conditions—are believed to be a rich source of cellulase and hemicellulase enzymes for lignocellulosic biomass deconstruction that are active at elevated temperatures and in the presence of pretreatment chemicals such as ionic liquids.

As part of their efforts to develop a cost-effective way to deconstruct lignocellulosic biomass into sugars for fuel, researchers in JBEI’s Deconstruction Division cultivated the switchgrass-feeding, compost-derived consortium of thermophiles.

To identify the functional roles of community members within the switchgrass-feeding consortium, the researchers first used shotgun sequencing, a metagenomics technique that enabled them to determine the metabolic potential of all the members of the consortium. They then used metaproteomic measurements to identify those enzymes, predicted by metagenomic analysis, that were actually produced by the microbial community.

While metagenomic sequences outlined the broad metabolic capabilities of the abundant populations present in the switchgrass adapted community, proteomic data allowed us to focus on the pathways that are actually expressed, and refine the assignment of roles for community members in biomass deconstruction.

—D’haeseleer et al.

Analysis of metagenomic sequencing data identified the most abundant microbial populations in the consortium to be closely related strains of Thermus thermophilus and Rhodothermus marinus. However, based on the assigned fractions of the switchgrass deconstruction proteome, the strains showing the most active role in switchgrass deconstruction were Gemmatimonadetes and Paenibacillus. By comparison, the more numerous Rhodothermus strain contributed fewer enzymes to biomass deconstruction.

By leveraging the unique capabilities of the JGI and EMSL with those at JBEI, we’re developing a more comprehensive functional understanding of how microbial consortia work to breakdown lignocellulose, and identifying the genes and enzymes that are responsible for this deconstruction. The list of genes and enzymes generated by this study has been placed into our expression pipeline and are being used to develop optimized cocktails that are capable of generating high sugar yields from pretreated lignocellulosic biomass.

—Blake Simmons, a chemical engineer who heads JBEI’s Deconstruction Division

JBEI is one of three Bioenergy Research Centers established by the DOE’s Office of Science in 2007. It is a scientific partnership led by Berkeley Lab and includes the Sandia National Laboratories, the University of California campuses of Berkeley and Davis, the Carnegie Institution for Science, and the Lawrence Livermore National Laboratory.


  • D’haeseleer P, Gladden JM, Allgaier M, Chain PSG, Tringe SG, et al. (2013) Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass. PLoS ONE 8(7): e68465. doi: 10.1371/journal.pone.0068465



Bio-fuels with a positive effect on GHG may eventually replace fossil fuels, specially for essential applications such as large airplanes etc.

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