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Enabling community-based metrology for wood-degrading fungi

Perez, Rolando and Luccioni, Marina and Kamakaka, Rohinton and Clamons, Samuel and Gaut, Nathaniel and Stirling, Finn and Adamala, Katarzyna P. and Silver, Pamela A. and Endy, Drew (2020) Enabling community-based metrology for wood-degrading fungi. Fungal Biology and Biotechnology, 7 (1). Art. No. 2. ISSN 2054-3085. PMCID PMC7081594. https://resolver.caltech.edu/CaltechAUTHORS:20200319-133757917

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1186/s40694-020-00092-2DOIArticle
https://doi.org/10.1101/815852DOIDiscussion Paper
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7081594PubMed CentralArticle
ORCID:
AuthorORCID
Clamons, Samuel0000-0002-7993-2278
Additional Information:© 2020 The Author(s). This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Received 04 December 2019; Accepted 25 February 2020; Published 19 March 2020. We thank Richard Murray for connecting us to his Caltech research group, Andrew Halleran for gathering interlaboratory data, Han Wosten for providing us with a sample of Schizophyllum commune, Phil Ross and Kabir Peay for discussions and advice, Jonathan Calles for discussions and editorial advice, Jensina Froland, Eden Grown-Haeberli, and Isaac Justice for help with pilot experiments, Cimeron Morrissey, Pawel Kusmierski, and Lin Feng for providing Pringles™ from Malaysia, Poland, and China, respectively, and Patrick Archie for providing compost from the Stanford Farm. Work supported by Stanford University unrestricted funds (D.E.); a National Science Foundation Graduate Research Fellowship (R.P.); the Stanford Enhancing Diversity in Graduate Education–Science, Technology, Engineering, and Mathematics Doctoral Fellowship Program (R.P.); the National Institute of Standards and Technology Joint Initiative for Metrology in Biology (D.E.); the Department of Systems Biology (F.S. and P.S.); the Wyss Institute for Biologically Inspired Engineering (F.S. and P.S.); the Institute for Collaborative Biotechnologies (U.S. A.R.O. Grant # W911NF-19-D-0001). Contributions: RP and DE conceived of the project, wrote, and edited the manuscript. RP performed the experiments and image and statistical analysis. ML performed pilot and commonly-used biomass experiments. NG, FS, SC, RK performed interlaboratory experiments. NG, FS, SC, RK, KA, PS edited the manuscript. All authors read and approved the final manuscript. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. The authors report no competing interests. Moreover, the work reported here does not reflect any position or policy of any government; no such endorsement should be inferred.
Funders:
Funding AgencyGrant Number
Stanford UniversityUNSPECIFIED
NSF Graduate Research FellowshipUNSPECIFIED
National Institute of Standards and Technology (NIST)UNSPECIFIED
Harvard UniversityUNSPECIFIED
Army Research Office (ARO)W911NF-19-D-0001
Subject Keywords:Synthetic biology; Mushrooms; Applied mycology; Biometrology; Literacy; Citizenship
Issue or Number:1
PubMed Central ID:PMC7081594
Record Number:CaltechAUTHORS:20200319-133757917
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20200319-133757917
Official Citation:Perez, R., Luccioni, M., Kamakaka, R. et al. Enabling community-based metrology for wood-degrading fungi. Fungal Biol Biotechnol 7, 2 (2020). https://doi.org/10.1186/s40694-020-00092-2
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:102003
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:19 Mar 2020 22:05
Last Modified:25 Mar 2020 15:27

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