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Smercina D, Zambare N, Hofmockel K, Sadler N, Bredeweg EL, Nicora C, Markillie LM, Aufrecht J. Synthetic Soil Aggregates: Bioprinted Habitats for High-Throughput Microbial Metaphenomics. Microorganisms 2022; 10:microorganisms10050944. [PMID: 35630387 PMCID: PMC9146112 DOI: 10.3390/microorganisms10050944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/20/2022] [Accepted: 04/28/2022] [Indexed: 02/01/2023] Open
Abstract
The dynamics of microbial processes are difficult to study in natural soil, owing to the small spatial scales on which microorganisms operate and to the opacity and chemical complexity of the soil habitat. To circumvent these challenges, we have created a 3D-bioprinted habitat that mimics aspects of natural soil aggregates while providing a chemically defined and translucent alternative culturing method for soil microorganisms. Our Synthetic Soil Aggregates (SSAs) retain the porosity, permeability, and patchy resource distribution of natural soil aggregates—parameters that are expected to influence emergent microbial community interactions. We demonstrate the printability and viability of several different microorganisms within SSAs and show how the SSAs can be integrated into a multi-omics workflow for single SSA resolution genomics, metabolomics, proteomics, lipidomics, and biogeochemical assays. We study the impact of the structured habitat on the distribution of a model co-culture microbial community and find that it is significantly different from the spatial organization of the same community in liquid culture, indicating a potential for SSAs to reproduce naturally occurring emergent community phenotypes. The SSAs have the potential as a tool to help researchers quantify microbial scale processes in situ and achieve high-resolution data from the interplay between environmental properties and microbial ecology.
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Aufrecht J, Khalid M, Walton CL, Tate K, Cahill JF, Retterer ST. Hotspots of root-exuded amino acids are created within a rhizosphere-on-a-chip. Lab Chip 2022; 22:954-963. [PMID: 35089295 DOI: 10.1039/d1lc00705j] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The rhizosphere is a challenging ecosystem to study from a systems biology perspective due to its diverse chemical, physical, and biological characteristics. In the past decade, microfluidic platforms (e.g. plant-on-a-chip) have created an alternative way to study whole rhizosphere organisms, like plants and microorganisms, under reduced-complexity conditions. However, in reducing the complexity of the environment, it is possible to inadvertently alter organism phenotype, which biases laboratory data compared to in situ experiments. To build back some of the complexity of the rhizosphere in a fully-defined, parameterized approach we have developed a rhizosphere-on-a-chip platform that mimics the physical structure of soil. We demonstrate, through computational simulation, how this synthetic soil structure can influence the emergence of molecular "hotspots" and "hotmoments" that arise naturally from the plant's exudation of labile carbon compounds. We establish the amenability of the rhizosphere-on-a-chip for long-term culture of Brachypodium distachyon, and experimentally validate the presence of exudate hotspots within the rhizosphere-on-a-chip pore spaces using liquid microjunction surface sampling probe mass spectrometry.
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Affiliation(s)
- Jayde Aufrecht
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Muneeba Khalid
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Courtney L Walton
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Kylee Tate
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - John F Cahill
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Scott T Retterer
- Center for Nanophase Materials Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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Millet LJ, Aufrecht J, Labbé J, Uehling J, Vilgalys R, Estes ML, Miquel Guennoc C, Deveau A, Olsson S, Bonito G, Doktycz MJ, Retterer ST. Increasing access to microfluidics for studying fungi and other branched biological structures. Fungal Biol Biotechnol 2019; 6:1. [PMID: 31198578 PMCID: PMC6556955 DOI: 10.1186/s40694-019-0071-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/15/2019] [Indexed: 01/01/2023] Open
Abstract
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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Affiliation(s)
- Larry J. Millet
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS 6445, Oak Ridge, TN 37831 USA
- The Bredesen Center, University of Tennessee-Knoxville, Knoxville, TN 37996 USA
| | - Jayde Aufrecht
- The Bredesen Center, University of Tennessee-Knoxville, Knoxville, TN 37996 USA
- The Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, PO Box 2008, MS 6445, Oak Ridge, TN 37831 USA
| | - Jessy Labbé
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS 6445, Oak Ridge, TN 37831 USA
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996 USA
| | - Jessie Uehling
- Biology Department, Duke University, Box 90338, Durham, NC 27708 USA
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA 94703 USA
| | - Rytas Vilgalys
- Biology Department, Duke University, Box 90338, Durham, NC 27708 USA
| | - Myka L. Estes
- The Center for Neuroscience, University of California Davis, One Shields Avenue, Davis, CA 95618 USA
| | - Cora Miquel Guennoc
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS 6445, Oak Ridge, TN 37831 USA
- Institut national de la recherche agronomique (INRA), Centre INRA-Lorraine, 54280 Champenoux, France
| | - Aurélie Deveau
- Institut national de la recherche agronomique (INRA), Centre INRA-Lorraine, 54280 Champenoux, France
| | - Stefan Olsson
- Fujian Agricultural and Forestry University, Fuzhou City, 350002 Fujian Province China
| | - Gregory Bonito
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824 USA
| | - Mitchel J. Doktycz
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS 6445, Oak Ridge, TN 37831 USA
- The Bredesen Center, University of Tennessee-Knoxville, Knoxville, TN 37996 USA
| | - Scott T. Retterer
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS 6445, Oak Ridge, TN 37831 USA
- The Bredesen Center, University of Tennessee-Knoxville, Knoxville, TN 37996 USA
- The Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, PO Box 2008, MS 6445, Oak Ridge, TN 37831 USA
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Timm CM, Pelletier DA, Jawdy SS, Gunter LE, Henning JA, Engle N, Aufrecht J, Gee E, Nookaew I, Yang Z, Lu TY, Tschaplinski TJ, Doktycz MJ, Tuskan GA, Weston DJ. Two Poplar-Associated Bacterial Isolates Induce Additive Favorable Responses in a Constructed Plant-Microbiome System. Front Plant Sci 2016; 7:497. [PMID: 27200001 PMCID: PMC4845692 DOI: 10.3389/fpls.2016.00497] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 03/29/2016] [Indexed: 05/18/2023]
Abstract
The biological function of the plant-microbiome system is the result of contributions from the host plant and microbiome members. The Populus root microbiome is a diverse community that has high abundance of β- and γ-Proteobacteria, both classes which include multiple plant-growth promoting representatives. To understand the contribution of individual microbiome members in a community, we studied the function of a simplified community consisting of Pseudomonas and Burkholderia bacterial strains isolated from Populus hosts and inoculated on axenic Populus cutting in controlled laboratory conditions. Both strains increased lateral root formation and root hair production in Arabidopsis plate assays and are predicted to encode for different functions related to growth and plant growth promotion in Populus hosts. Inoculation individually, with either bacterial isolate, increased root growth relative to uninoculated controls, and while root area was increased in mixed inoculation, the interaction term was insignificant indicating additive effects of root phenotype. Complementary data including photosynthetic efficiency, whole-transcriptome gene expression and GC-MS metabolite expression data in individual and mixed inoculated treatments indicate that the effects of these bacterial strains are unique and additive. These results suggest that the function of a microbiome community may be predicted from the additive functions of the individual members.
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Affiliation(s)
- Collin M. Timm
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
- *Correspondence: Collin M. Timm
| | - Dale A. Pelletier
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Sara S. Jawdy
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Lee E. Gunter
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Jeremiah A. Henning
- Department of Ecology and Evolutionary Biology, University of TennesseeKnoxville, TN, USA
| | - Nancy Engle
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Jayde Aufrecht
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of TennesseeKnoxville, TN, USA
| | - Emily Gee
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Intawat Nookaew
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Zamin Yang
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Tse-Yuan Lu
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | | | | | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - David J. Weston
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
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