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Sher AW, Aufrecht JA, Herrera D, Zimmerman AE, Kim YM, Munoz N, Trejo JB, Paurus VL, Cliff JB, Hu D, Chrisler WB, Tournay RJ, Gomez-Rivas E, Orr G, Ahkami AH, Doty SL. Dynamic nitrogen fixation in an aerobic endophyte of Populus. ISME J 2024; 18:wrad012. [PMID: 38365250 PMCID: PMC10833079 DOI: 10.1093/ismejo/wrad012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/11/2023] [Accepted: 11/21/2023] [Indexed: 02/18/2024]
Abstract
Biological nitrogen fixation by microbial diazotrophs can contribute significantly to nitrogen availability in non-nodulating plant species. In this study of molecular mechanisms and gene expression relating to biological nitrogen fixation, the aerobic nitrogen-fixing endophyte Burkholderia vietnamiensis, strain WPB, isolated from Populus trichocarpa served as a model for endophyte-poplar interactions. Nitrogen-fixing activity was observed to be dynamic on nitrogen-free medium with a subset of colonies growing to form robust, raised globular like structures. Secondary ion mass spectrometry (NanoSIMS) confirmed that N-fixation was uneven within the population. A fluorescent transcriptional reporter (GFP) revealed that the nitrogenase subunit nifH is not uniformly expressed across genetically identical colonies of WPB and that only ~11% of the population was actively expressing the nifH gene. Higher nifH gene expression was observed in clustered cells through monitoring individual bacterial cells using single-molecule fluorescence in situ hybridization. Through 15N2 enrichment, we identified key nitrogenous metabolites and proteins synthesized by WPB and employed targeted metabolomics in active and inactive populations. We cocultivated WPB Pnif-GFP with poplar within a RhizoChip, a synthetic soil habitat, which enabled direct imaging of microbial nifH expression within root epidermal cells. We observed that nifH expression is localized to the root elongation zone where the strain forms a unique physical interaction with the root cells. This work employed comprehensive experimentation to identify novel mechanisms regulating both biological nitrogen fixation and beneficial plant-endophyte interactions.
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Affiliation(s)
- Andrew W Sher
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA, 98195-2100, United States
| | - Jayde A Aufrecht
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Daisy Herrera
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Amy E Zimmerman
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Nathalie Munoz
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Jesse B Trejo
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Vanessa L Paurus
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - John B Cliff
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Dehong Hu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - William B Chrisler
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Robert J Tournay
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA, 98195-2100, United States
| | - Emma Gomez-Rivas
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA, 98195-2100, United States
| | - Galya Orr
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Amir H Ahkami
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Sharon L Doty
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA, 98195-2100, United States
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Uehling JK, Entler MR, Meredith HR, Millet LJ, Timm CM, Aufrecht JA, Bonito GM, Engle NL, Labbé JL, Doktycz MJ, Retterer ST, Spatafora JW, Stajich JE, Tschaplinski TJ, Vilgalys RJ. Microfluidics and Metabolomics Reveal Symbiotic Bacterial-Fungal Interactions Between Mortierella elongata and Burkholderia Include Metabolite Exchange. Front Microbiol 2019; 10:2163. [PMID: 31632357 PMCID: PMC6779839 DOI: 10.3389/fmicb.2019.02163] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/03/2019] [Indexed: 01/12/2023] Open
Abstract
We identified two poplar (Populus sp.)-associated microbes, the fungus, Mortierella elongata strain AG77, and the bacterium, Burkholderia strain BT03, that mutually promote each other’s growth. Using culture assays in concert with a novel microfluidic device to generate time-lapse videos, we found growth specific media differing in pH and pre-conditioned by microbial growth led to increased fungal and bacterial growth rates. Coupling microfluidics and comparative metabolomics data results indicated that observed microbial growth stimulation involves metabolic exchange during two ordered events. The first is an emission of fungal metabolites, including organic acids used or modified by bacteria. A second signal of unknown nature is produced by bacteria which increases fungal growth rates. We find this symbiosis is initiated in part by metabolic exchange involving fungal organic acids.
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Affiliation(s)
- Jessie K Uehling
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States.,Department of Biology, Duke University, Durham, NC, United States
| | - Matthew R Entler
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Hannah R Meredith
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States.,Department of Biomedical Engineering, Duke University, Durham, NC, United States
| | - Larry J Millet
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,The Bredesen Center, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Collin M Timm
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jayde A Aufrecht
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Gregory M Bonito
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Nancy L Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jessy L Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Genome Science & Technology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Genome Science & Technology, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Scott T Retterer
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
| | | | - Rytas J Vilgalys
- Department of Biology, Duke University, Durham, NC, United States
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Aufrecht JA, Timm CM, Bible A, Morrell-Falvey JL, Pelletier DA, Doktycz MJ, Retterer ST. Microfluidics: Quantifying the Spatiotemporal Dynamics of Plant Root Colonization by Beneficial Bacteria in a Microfluidic Habitat (Adv. Biosys. 6/2018). ACTA ACUST UNITED AC 2018. [DOI: 10.1002/adbi.201870051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jayde A. Aufrecht
- Bioscience Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
- Bredesen Center; University of Tennessee; Knoxville TN 37996 USA
| | - Collin M. Timm
- Bioscience Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - Amber Bible
- Biochemistry and Cellular and Molecular Biology; University of Tennessee; Knoxville TN 37996 USA
| | - Jennifer L. Morrell-Falvey
- Bioscience Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
- Bredesen Center; University of Tennessee; Knoxville TN 37996 USA
- Biochemistry and Cellular and Molecular Biology; University of Tennessee; Knoxville TN 37996 USA
| | - Dale A. Pelletier
- Bioscience Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - Mitchel J. Doktycz
- Bioscience Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
- Bredesen Center; University of Tennessee; Knoxville TN 37996 USA
- Center for Nanophase Materials Sciences; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - Scott T. Retterer
- Bioscience Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
- Bredesen Center; University of Tennessee; Knoxville TN 37996 USA
- Center for Nanophase Materials Sciences; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
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Aufrecht JA, Timm CM, Bible A, Morrell‐Falvey JL, Pelletier DA, Doktycz MJ, Retterer ST. Quantifying the Spatiotemporal Dynamics of Plant Root Colonization by Beneficial Bacteria in a Microfluidic Habitat. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/adbi.201800048] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jayde A. Aufrecht
- Bioscience Division Oak Ridge National Laboratory Oak Ridge TN 37831 USA
- Bredesen Center University of Tennessee Knoxville TN 37996 USA
| | - Collin M. Timm
- Bioscience Division Oak Ridge National Laboratory Oak Ridge TN 37831 USA
| | - Amber Bible
- Biochemistry and Cellular and Molecular Biology University of Tennessee Knoxville TN 37996 USA
| | - Jennifer L. Morrell‐Falvey
- Bioscience Division Oak Ridge National Laboratory Oak Ridge TN 37831 USA
- Bredesen Center University of Tennessee Knoxville TN 37996 USA
- Biochemistry and Cellular and Molecular Biology University of Tennessee Knoxville TN 37996 USA
| | - Dale A. Pelletier
- Bioscience Division Oak Ridge National Laboratory Oak Ridge TN 37831 USA
| | - Mitchel J. Doktycz
- Bioscience Division Oak Ridge National Laboratory Oak Ridge TN 37831 USA
- Bredesen Center University of Tennessee Knoxville TN 37996 USA
- Center for Nanophase Materials Sciences Oak Ridge National Laboratory Oak Ridge TN 37831 USA
| | - Scott T. Retterer
- Bioscience Division Oak Ridge National Laboratory Oak Ridge TN 37831 USA
- Bredesen Center University of Tennessee Knoxville TN 37996 USA
- Center for Nanophase Materials Sciences Oak Ridge National Laboratory Oak Ridge TN 37831 USA
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5
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Shankles PG, Millet LJ, Aufrecht JA, Retterer ST. Accessing microfluidics through feature-based design software for 3D printing. PLoS One 2018; 13:e0192752. [PMID: 29596418 PMCID: PMC5875762 DOI: 10.1371/journal.pone.0192752] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/30/2018] [Indexed: 01/11/2023] Open
Abstract
Additive manufacturing has been a cornerstone of the product development pipeline for decades, playing an essential role in the creation of both functional and cosmetic prototypes. In recent years, the prospects for distributed and open source manufacturing have grown tremendously. This growth has been enabled by an expanding library of printable materials, low-cost printers, and communities dedicated to platform development. The microfluidics community has embraced this opportunity to integrate 3D printing into the suite of manufacturing strategies used to create novel fluidic architectures. The rapid turnaround time and low cost to implement these strategies in the lab makes 3D printing an attractive alternative to conventional micro- and nanofabrication techniques. In this work, the production of multiple microfluidic architectures using a hybrid 3D printing-soft lithography approach is demonstrated and shown to enable rapid device fabrication with channel dimensions that take advantage of laminar flow characteristics. The fabrication process outlined here is underpinned by the implementation of custom design software with an integrated slicer program that replaces less intuitive computer aided design and slicer software tools. Devices are designed in the program by assembling parameterized microfluidic building blocks. The fabrication process and flow control within 3D printed devices were demonstrated with a gradient generator and two droplet generator designs. Precise control over the printing process allowed 3D microfluidics to be printed in a single step by extruding bridge structures to ‘jump-over’ channels in the same plane. This strategy was shown to integrate with conventional nanofabrication strategies to simplify the operation of a platform that incorporates both nanoscale features and 3D printed microfluidics.
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Affiliation(s)
- Peter G. Shankles
- The Bredesen Center for Interdisciplinary Research, The University of Tennessee, Knoxville, TN, United States of America
| | - Larry J. Millet
- The Bredesen Center for Interdisciplinary Research, The University of Tennessee, Knoxville, TN, United States of America
| | - Jayde A. Aufrecht
- The Bredesen Center for Interdisciplinary Research, The University of Tennessee, Knoxville, TN, United States of America
| | - Scott T. Retterer
- The Bredesen Center for Interdisciplinary Research, The University of Tennessee, Knoxville, TN, United States of America
- The Center for Nanophase Materials Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
- * E-mail:
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6
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Aufrecht JA, Ryan JM, Hasim S, Allison DP, Nebenführ A, Doktycz MJ, Retterer ST. Imaging the Root Hair Morphology of Arabidopsis Seedlings in a Two-layer Microfluidic Platform. J Vis Exp 2017. [PMID: 28829431 DOI: 10.3791/55971] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Root hairs increase root surface area for better water uptake and nutrient absorption by the plant. Because they are small in size and often obscured by their natural environment, root hair morphology and function are difficult to study and often excluded from plant research. In recent years, microfluidic platforms have offered a way to visualize root systems at high resolution without disturbing the roots during transfer to an imaging system. The microfluidic platform presented here builds on previous plant-on-a-chip research by incorporating a two-layer device to confine the Arabidopsis thaliana main root to the same optical plane as the root hairs. This design enables the quantification of root hairs on a cellular and organelle level and also prevents z-axis drifting during the addition of experimental treatments. We describe how to store the devices in a contained and hydrated environment, without the need for fluidic pumps, while maintaining a gnotobiotic environment for the seedling. After the optical imaging experiment, the device may be disassembled and used as a substrate for atomic force or scanning electron microscopy while keeping fine root structures intact.
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Affiliation(s)
- Jayde A Aufrecht
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee; Bioscience Division and Center for Nanophase Materials Sciences, Oak Ridge national Laboratory
| | - Jennifer M Ryan
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee
| | - Sahar Hasim
- Department of Microbiology, University of Tennessee
| | - David P Allison
- Bioscience Division and Center for Nanophase Materials Sciences, Oak Ridge national Laboratory; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee
| | - Andreas Nebenführ
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee
| | - Mitchel J Doktycz
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee; Bioscience Division and Center for Nanophase Materials Sciences, Oak Ridge national Laboratory
| | - Scott T Retterer
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee; Bioscience Division and Center for Nanophase Materials Sciences, Oak Ridge national Laboratory;
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