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Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme Discovery in Lignocellulolytic Microbial Communities |
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| Authors: | Kristen M. DeAngelis John M. Gladden Martin Allgaier Patrik D’haeseleer Julian L. Fortney Amitha Reddy Philip Hugenholtz Steven W. Singer Jean S. Vander Gheynst Whendee L. Silver Blake A. Simmons Terry C. Hazen |
| Affiliation: | 1. Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA 2. Earth Sciences Division, Lawrence Berkeley National Lab, Berkeley, CA, USA 3. Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA 4. Joint Genome Institute, Walnut Creek, CA, USA 5. Department of Biological and Agricultural Engineering, University of California, Davis, CA, USA 6. Ecosystem Sciences, Policy and Management, University of California, Berkeley, CA, USA 7. Biomass Science and Conversion Technology Department, Sandia National Laboratory, Livermore, CA, USA 8. Ecology Department, Earth Sciences Division, Lawrence Berkeley National Lab, One Cyclotron Road MS 70A-3317, Berkeley, CA, 94720, USA |
| Abstract: | Producing cellulosic biofuels from plant material has recently emerged as a key US Department of Energy goal. For this technology to be commercially viable on a large scale, it is critical to make production cost efficient by streamlining both the deconstruction of lignocellulosic biomass and fuel production. Many natural ecosystems efficiently degrade lignocellulosic biomass and harbor enzymes that, when identified, could be used to increase the efficiency of commercial biomass deconstruction. However, ecosystems most likely to yield relevant enzymes, such as tropical rain forest soil in Puerto Rico, are often too complex for enzyme discovery using current metagenomic sequencing technologies. One potential strategy to overcome this problem is to selectively cultivate the microbial communities from these complex ecosystems on biomass under defined conditions, generating less complex biomass-degrading microbial populations. To test this premise, we cultivated microbes from Puerto Rican soil or green waste compost under precisely defined conditions in the presence dried ground switchgrass (Panicum virgatum L.) or lignin, respectively, as the sole carbon source. Phylogenetic profiling of the two feedstock-adapted communities using SSU rRNA gene amplicon pyrosequencing or phylogenetic microarray analysis revealed that the adapted communities were significantly simplified compared to the natural communities from which they were derived. Several members of the lignin-adapted and switchgrass-adapted consortia are related to organisms previously characterized as biomass degraders, while others were from less well-characterized phyla. The decrease in complexity of these communities make them good candidates for metagenomic sequencing and will likely enable the reconstruction of a greater number of full-length genes, leading to the discovery of novel lignocellulose-degrading enzymes adapted to feedstocks and conditions of interest. |
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