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J Microbiol Biol Educ. 2019 Jul 26;20(2). pii: 20.2.34. doi: 10.1128/jmbe.v20i2.1723. eCollection 2019.

Isolation and Characterization of Bacterial Cellulase Producers for Biomass Deconstruction: A Microbiology Laboratory Course.

Barajas JF1,2, Wehrs M2,3, To M2,3, Cruickshanks L4, Urban R2,3,5, McKee A2,3,6, Gladden J7, Goh EB2,3,8, Brown ME2,3,9, Pierotti D2,3, Carothers JM10, Mukhopadhyay A2,3, Keasling JD2,3,10,11,12,13,14,15, Fortman JL2,3,15, Singer SW2,3, Bailey CB2,3,11.

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Agile BioFoundry, Emeryville, CA 94608.
Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
Joint BioEnergy Institute, Emeryville, CA 94608.
Oakland Technical High School, Oakland, CA 94611.
University of Southern California Viterbi School of Engineering, Los Angeles, CA 90089.
Helix OpCo, San Carlos, CA 94070.
Sandia National Laboratories, Livermore CA 94551.
Lygos Inc., Berkeley, CA 94710.
MicroByre, Berkeley, CA 94720.
Department of Chemical Engineering, University of Washington, Seattle, WA 98195.
QB3 Institute, University of California-Berkeley, Emeryville, CA 94608.
University of California, Berkeley, Department of Chemical & Biomolecular Engineering, Berkeley, CA 94720.
University of California, Berkeley, Department of Bioengineering, Berkeley, CA 94720.
Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, DK2970-Horsholm, Denmark.
Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China.


The conversion of biomass to biofuels presents a solution to one of the largest global challenges of our era, climate change. A critical part of this pipeline is the process of breaking down cellulosic sugars from plant matter to be used by microbes containing biosynthetic pathways that produce biofuels or bioproducts. In this inquiry-based course, students complete a research project that isolates cellulase-producing bacteria from samples collected from the environment. After obtaining isolates, the students characterize the production of cellulases. Students then amplify and sequence the 16S rRNA genes of confirmed cellulase producers and use bioinformatic methods to identify the bacterial isolates. Throughout the course, students learn about the process of generating biofuels and bioproducts through the deconstruction of cellulosic biomass to form monosaccharides from the biopolymers in plant matter. The program relies heavily on active learning and enables students to connect microbiology with issues of sustainability. In addition, it provides exposure to basic microbiology, molecular biology, and biotechnology laboratory techniques and concepts. The described activity was initially developed for the Introductory College Level Experience in Microbiology (iCLEM) program, a research-based immersive laboratory course at the US Department of Energy Joint BioEnergy Institute. Originally designed as an accelerated program for high-potential, low-income, high school students (11th-12th grade), this curriculum could also be implemented for undergraduate coursework in a research-intensive laboratory course at a two- or four-year college or university.

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