Enabling community-based metrology for wood-degrading fungi

Springer Science and Business Media LLC - 2020
Rolando Perez1, Marina Luccioni1, Rohinton T. Kamakaka2, Samuel Clamons3, Nathaniel J. Gaut4, Finn Stirling5, Katarzyna P. Adamala4, Pamela A. Silver5, Drew Endy1
1Department of Bioengineering, Schools of Engineering and Medicine, Stanford University, Room 252, Shriram Center, 443 Via Ortega, Stanford, CA, 94305, USA
2Department of MCD Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
3Department of Chemistry and Molecular Biophysics, California Institute of Technology, 1200 E. California Blvd, MC 138-78, Pasadena, CA, 91125, USA
4Department of Genetics, Cell Biology, and Development, College of Biological Sciences, University of Minnesota, 420 Washington Ave. SE, 5-178 MCB, Minneapolis, MN, 55455, USA
5Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Warren Alpert Building, Boston, MA, 02115, USA

Tóm tắt

Abstract Background Lignocellulosic biomass could support a greatly-expanded bioeconomy. Current strategies for using biomass typically rely on single-cell organisms and extensive ancillary equipment to produce precursors for downstream manufacturing processes. Alternative forms of bioproduction based on solid-state fermentation and wood-degrading fungi could enable more direct means of manufacture. However, basic methods for cultivating wood-degrading fungi are often ad hoc and not readily reproducible. Here, we developed standard reference strains, substrates, measurements, and methods sufficient to begin to enable reliable reuse of mycological materials and products in simple laboratory settings. Results We show that a widely-available and globally-regularized consumer product (Pringles™) can support the growth of wood-degrading fungi, and that growth on Pringles™-broth can be correlated with growth on media made from a fully-traceable and compositionally characterized substrate (National Institute of Standards and Technology Reference Material 8492 Eastern Cottonwood Whole Biomass Feedstock). We also establish a Relative Extension Unit (REU) framework that is designed to reduce variation in quantification of radial growth measurements. So enabled, we demonstrate that five laboratories were able to compare measurements of wood-fungus performance via a simple radial extension growth rate assay, and that our REU-based approach reduced variation in reported measurements by up to ~ 75%. Conclusions Reliable reuse of materials, measures, and methods is necessary to enable distributed bioproduction processes that can be adopted at all scales, from local to industrial. Our community-based measurement methods incentivize practitioners to coordinate the reuse of standard materials, methods, strains, and to share information supporting work with wood-degrading fungi.

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