Increasing access to microfluidics for studying fungi and other branched biological structures

Millet, Larry J.; Aufrecht, Jayde; Labbé, Jessy; Uehling, Jessie; Vilgalys, Rytas; Estes, Myka L.; Miquel Guennoc, Cora; Deveau, Aurélie; Olsson, Stefan; Bonito, Gregory; Doktycz, Mitchel John; Retterer, Scott T.

doi:10.1186/s40694-019-0071-z

Title: Increasing access to microfluidics for studying fungi and other branched biological structures

Journal Article · 10 June 2019 · Fungal Biology and Biotechnology

DOI: https://doi.org/10.1186/s40694-019-0071-z · OSTI ID:1528740

^[1]; Aufrecht, Jayde ^[2];

^[3]; Uehling, Jessie ^[4]; Vilgalys, Rytas ^[5]; Estes, Myka L. ^[6]; Miquel Guennoc, Cora ^[7]; Deveau, Aurélie ^[8]; Olsson, Stefan ^[9]; Bonito, Gregory ^[10];

^[1];

^[11]

Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Univ. of Tennessee, Knoxville, TN (United States). Bredesen Center
Univ. of Tennessee, Knoxville, TN (United States). Bredesen Center; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Nanophase Materials Science (CNMS)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Univ. of Tennessee, Knoxville, TN (United States). Dept. of Biochemistry and Cellular and Molecular Biology
Duke Univ., Durham, NC (United States). Biology Dept.; Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology
Duke Univ., Durham, NC (United States). Biology Dept.
Univ. of California, Davis, CA (United States). Center for Neuroscience
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Inst. national de la recherche agronomique (INRA), Centre INRA-Lorraine, Champenoux (France)
Inst. national de la recherche agronomique (INRA), Centre INRA-Lorraine, Champenoux (France)
Fujian Agricultural and Forestry Univ., Fuzhou City (China)
Michigan State Univ., East Lansing, MI (United States). Dept. of Plant, Soil and Microbial Sciences
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Univ. of Tennessee, Knoxville, TN (United States). Bredesen Center; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Nanophase Materials Science (CNMS)

Background: Microfluidic systems are well-suited for studying mixed biological communities for improving industrial processes of fermentation, biofuel production, and pharmaceutical production. The results of which have the potential to resolve the underlying mechanisms of growth and transport in these complex branched living systems. Microfluidics provide controlled environments and improved optical access for real-time and high-resolution imaging studies that allow high-content and quantitative analyses. Studying growing branched structures and the dynamics of cellular interactions with both biotic and abiotic cues provides context for molecule production and genetic manipulations. To make progress in this arena, technical and logistical barriers must be overcome to more effectively deploy microfluidics in biological disciplines. A principle technical barrier is the process of assembling, sterilizing, and hydrating the microfluidic system; the lack of the necessary equipment for the preparatory process is a contributing factor to this barrier. To improve access to microfluidic systems, we present the development, characterization, and implementation of a microfluidics assembly and packaging process that builds on self-priming point-of-care principles to achieve “ready-to-use microfluidics.”Results: We present results from domestic and international collaborations using novel microfluidic architectures prepared with a unique packaging protocol. We implement this approach by focusing primarily on filamentous fungi; we also demonstrate the utility of this approach for collaborations on plants and neurons. In this work we (1) determine the shelf-life of ready-to-use microfluidics, (2) demonstrate biofilm-like colonization on fungi, (3) describe bacterial motility on fungal hyphae (fungal highway), (4) report material-dependent bacterial-fungal colonization, (5) demonstrate germination of vacuum-sealed Arabidopsis seeds in microfluidics stored for up to 2 weeks, and (6) observe bidirectional cytoplasmic streaming in fungi.Conclusions: This pre-packaging approach provides a simple, one step process to initiate microfluidics in any setting for fungal studies, bacteria-fungal interactions, and other biological inquiries. This process improves access to microfluidics for controlling biological microenvironments, and further enabling visual and quantitative analysis of fungal cultures.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1528740

Journal Information:: Fungal Biology and Biotechnology, Vol. 6, Issue 1; ISSN 2054-3085

Country of Publication:: United States

Language:: English

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Patterning Mechanisms of Branched Organs Lu, P.; Werb, Z. Science, Vol. 322, Issue 5907 https://doi.org/10.1126/science.1162783	journal	December 2008
Asymmetric illumination contrast: a method of image formation for video light microscopy Kachar, B. Science, Vol. 227, Issue 4688 https://doi.org/10.1126/science.3969565	journal	February 1985
Spatiometabolic Stratification of Shewanella oneidensis Biofilms Teal, T. K.; Lies, D. P.; Wold, B. J. Applied and Environmental Microbiology, Vol. 72, Issue 11 https://doi.org/10.1128/aem.01163-06	journal	August 2006
Nonribosomal Peptides, Key Biocontrol Components for Pseudomonas fluorescens In5, Isolated from a Greenlandic Suppressive Soil Michelsen, Charlotte F.; Watrous, Jeramie; Glaring, Mikkel A. mBio, Vol. 6, Issue 2 https://doi.org/10.1128/mbio.00079-15	journal	March 2015
Droplet-based microfluidic high-throughput screening of heterologous enzymes secreted by the yeast Yarrowia lipolytica Beneyton, Thomas; Thomas, Stéphane; Griffiths, Andrew D. Microbial Cell Factories, Vol. 16, Issue 1 https://doi.org/10.1186/s12934-017-0629-5	journal	January 2017
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A microfluidic device for measuring cell migration towards substrate-bound and soluble chemokine gradients Schwarz, Jan; Bierbaum, Veronika; Merrin, Jack ETH Zurich https://doi.org/10.3929/ethz-b-000122693	text	January 2016
Increasing access to microfluidics for studying fungi and other branched biological structures Millet, Larry; Aufrecht, Jayde; Labbé, Jessy Figshare https://doi.org/10.6084/m9.figshare.c.4534424	collection	January 2019

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Growing a circular economy with fungal biotechnology: a white paper Meyer, Vera; Basenko, Evelina Y.; Benz, J. Philipp Fungal Biology and Biotechnology, Vol. 7, Issue 1 https://doi.org/10.1186/s40694-020-00095-z	journal	April 2020

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MOESM1 of Increasing access to microfluidics for studying fungi and other branched biological structures Millet, Larry; Aufrecht, Jayde; LabbĂŠ, Jessy https://doi.org/10.6084/m9.figshare.8247248 The current record is supplemented by this text	text	January 2019
MOESM1 of Increasing access to microfluidics for studying fungi and other branched biological structures Millet, Larry; Aufrecht, Jayde; LabbĂŠ, Jessy https://doi.org/10.6084/m9.figshare.8247248.v1 The current record is supplemented by this text	text	January 2019
MOESM2 of Increasing access to microfluidics for studying fungi and other branched biological structures Millet, Larry; Aufrecht, Jayde; LabbĂŠ, Jessy https://doi.org/10.6084/m9.figshare.8247254 The current record is supplemented by this text	text	January 2019
MOESM2 of Increasing access to microfluidics for studying fungi and other branched biological structures Millet, Larry; Aufrecht, Jayde; LabbĂŠ, Jessy https://doi.org/10.6084/m9.figshare.8247254.v1 The current record is supplemented by this text	text	January 2019
MOESM3 of Increasing access to microfluidics for studying fungi and other branched biological structures Millet, Larry; Aufrecht, Jayde; Labbé, Jessy https://doi.org/10.6084/m9.figshare.8247260 The current record is supplemented by this text	text	January 2019
MOESM3 of Increasing access to microfluidics for studying fungi and other branched biological structures Millet, Larry; Aufrecht, Jayde; Labbé, Jessy https://doi.org/10.6084/m9.figshare.8247260.v1 The current record is supplemented by this text	text	January 2019
MOESM4 of Increasing access to microfluidics for studying fungi and other branched biological structures Millet, Larry; Aufrecht, Jayde; LabbĂŠ, Jessy https://doi.org/10.6084/m9.figshare.8247272 The current record is supplemented by this text	text	January 2019
MOESM4 of Increasing access to microfluidics for studying fungi and other branched biological structures Millet, Larry; Aufrecht, Jayde; LabbĂŠ, Jessy https://doi.org/10.6084/m9.figshare.8247272.v1 The current record is supplemented by this text	text	January 2019
Increasing access to microfluidics for studying fungi and other branched biological structures Millet, Larry; Aufrecht, Jayde; Labbé, Jessy https://doi.org/10.6084/m9.figshare.c.4534424 The current record is supplemented by this collection	collection	January 2019
Increasing access to microfluidics for studying fungi and other branched biological structures Millet, Larry; Aufrecht, Jayde; Labbé, Jessy https://doi.org/10.6084/m9.figshare.c.4534424.v1 The current record is supplemented by this collection	collection	January 2019