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Guichard M, Holla S, Wernerová D, Grossmann G, Minina EA. RoPod, a customizable toolkit for non-invasive root imaging, reveals cell type-specific dynamics of plant autophagy. Sci Rep 2024; 14:12664. [PMID: 38830985 PMCID: PMC11148066 DOI: 10.1038/s41598-024-63226-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 05/24/2024] [Indexed: 06/05/2024] Open
Abstract
Arabidopsis root is a classic model system in plant cell and molecular biology. The sensitivity of plant roots to local environmental perturbation challenges data reproducibility and incentivizes further optimization of imaging and phenotyping tools. Here we present RoPod, an easy-to-use toolkit for low-stress live time-lapse imaging of Arabidopsis roots. RoPod comprises a dedicated protocol for plant cultivation and a customizable 3D-printed vessel with integrated microscopy-grade glass that serves simultaneously as a growth and imaging chamber. RoPod reduces impact of sample handling, preserves live samples for prolonged imaging sessions, and facilitates application of treatments during image acquisition. We describe a protocol for RoPods fabrication and provide illustrative application pipelines for monitoring root hair growth and autophagic activity. Furthermore, we showcase how the use of RoPods advanced our understanding of plant autophagy, a major catabolic pathway and a key player in plant fitness. Specifically, we obtained fine time resolution for autophagy response to commonly used chemical modulators of the pathway and revealed previously overlooked cell type-specific changes in the autophagy response. These results will aid a deeper understanding of the physiological role of autophagy and provide valuable guidelines for choosing sampling time during end-point assays currently employed in plant autophagy research.
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Affiliation(s)
- Marjorie Guichard
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany.
- Institute of Cell and Interaction Biology, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany.
- CEPLAS Cluster of Excellence on Plant Sciences, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany.
| | - Sanjana Holla
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, P.O. Box 7015, SE-750 07, Uppsala, Sweden
| | - Daša Wernerová
- Institute of Cell and Interaction Biology, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany
| | - Guido Grossmann
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
- Institute of Cell and Interaction Biology, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany
- CEPLAS Cluster of Excellence on Plant Sciences, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany
| | - Elena A Minina
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany.
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, P.O. Box 7015, SE-750 07, Uppsala, Sweden.
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2
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Ugolini GS, Wang M, Secchi E, Pioli R, Ackermann M, Stocker R. Microfluidic approaches in microbial ecology. LAB ON A CHIP 2024; 24:1394-1418. [PMID: 38344937 PMCID: PMC10898419 DOI: 10.1039/d3lc00784g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Microbial life is at the heart of many diverse environments and regulates most natural processes, from the functioning of animal organs to the cycling of global carbon. Yet, the study of microbial ecology is often limited by challenges in visualizing microbial processes and replicating the environmental conditions under which they unfold. Microfluidics operates at the characteristic scale at which microorganisms live and perform their functions, thus allowing for the observation and quantification of behaviors such as growth, motility, and responses to external cues, often with greater detail than classical techniques. By enabling a high degree of control in space and time of environmental conditions such as nutrient gradients, pH levels, and fluid flow patterns, microfluidics further provides the opportunity to study microbial processes in conditions that mimic the natural settings harboring microbial life. In this review, we describe how recent applications of microfluidic systems to microbial ecology have enriched our understanding of microbial life and microbial communities. We highlight discoveries enabled by microfluidic approaches ranging from single-cell behaviors to the functioning of multi-cellular communities, and we indicate potential future opportunities to use microfluidics to further advance our understanding of microbial processes and their implications.
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Affiliation(s)
- Giovanni Stefano Ugolini
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Miaoxiao Wang
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland
| | - Eleonora Secchi
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Roberto Pioli
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Martin Ackermann
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland
- Laboratory of Microbial Systems Ecology, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédéral de Lausanne (EPFL), Lausanne, Switzerland
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
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3
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Conway JM, Martinez PJ, Wilson ED, Del Risco NM, Dangl JL. Arabidopsis Root Microbiome Microfluidic (ARMM) Device for Imaging Bacterial Colonization and Morphogenesis of Arabidopsis Roots. Methods Mol Biol 2024; 2805:213-228. [PMID: 39008185 DOI: 10.1007/978-1-0716-3854-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Imaging the spatiotemporal dynamics of host-microbiota interactions is of particular interest for augmenting our understanding of these complex systems. This is especially true of plant-microbe interactions happening around, on, and inside plant roots where relatively little is understood about the dynamics of these systems. Over the past decade, a number of microfluidic devices have been developed to grow plants hydroponically in gnotobiotic conditions and image morphogenesis of the root and/or dynamics with fluorescently labeled bacteria from the plant root microbiome. Here we describe the construction and use of our Arabidopsis Root Microbiome Microfluidic (ARMM) device for imaging fluorescent protein expressing bacteria and their colonization of Arabidopsis roots. In contrast to other plant root imaging devices, we designed this device to have a larger chamber for observing Arabidopsis root elongation and plant-microbe interactions with older seedlings (between 1.5 and 4 weeks after germination) and a 200 μm chamber depth to specifically maintain thin Arabidopsis roots within the focal distance of the confocal microscope. Our device incorporates a new approach to growing Arabidopsis seedlings in screw-top tube caps for simplified germination and transfer to the device. We present representative images from the ARMM device including high resolution cross section images of bacterial colonization at the root surface.
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Affiliation(s)
- Jonathan M Conway
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA.
| | - Payton J Martinez
- Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biomedical Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Ellie D Wilson
- Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nicole M Del Risco
- Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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4
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Kaduchová K, Čmiel V, Koláčková V, Pecinka A. EasyClick: an improved system for confocal microscopy of live roots with a user-optimized sample holder. PLANTA 2023; 259:22. [PMID: 38095727 PMCID: PMC10721658 DOI: 10.1007/s00425-023-04293-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/14/2023] [Indexed: 12/17/2023]
Abstract
MAIN CONCLUSION We describe a user-optimized sample holder EasyClick for medium-sized plants that reduces root side movements and thus greatly extends the duration of live cell confocal microscopy. Preparation and mounting of the samples are key factors for successful live cell microscopy. To acquire biologically relevant data, it is necessary to minimize stress and avoid physical damage to plant tissues during the installation of the sample into the microscope. This is challenging, particularly when the whole plant is mounted as the living sample needs to be properly anchored in the microscopic system to obtain high-quality and high-resolution data. Here, we present a user-optimized sample holder EasyClick for live cell inverted confocal microscopic analysis of plant roots with diameters from 0.3 to 0.7 mm. The EasyClick holder was tested on an inverted confocal microscope using germinating plants of several cereals. Nevertheless, it can be directly used on other types of inverted microscopes from various producers and on different plant species. The EasyClick holder effectively restricts root lateral and vertical movements. This greatly improves the conditions for time-lapse microscopy of the samples of interest.
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Affiliation(s)
- Kateřina Kaduchová
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00, Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, 779 00, Olomouc, Czech Republic
| | - Vratislav Čmiel
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technická 3082/12, 61600, Brno, Czech Republic.
| | - Veronika Koláčková
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00, Olomouc, Czech Republic
| | - Ales Pecinka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00, Olomouc, Czech Republic.
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5
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Kaiser CF, Perilli A, Grossmann G, Meroz Y. Studying root-environment interactions in structured microdevices. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad122. [PMID: 37042515 PMCID: PMC10353529 DOI: 10.1093/jxb/erad122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Indexed: 06/19/2023]
Abstract
In negotiating with the environment, plant roots integrate sensory information over space and time, as the basis of decision making in roots under non-uniform conditions. The complexity and dynamic properties of soil across spatial and temporal scales pose a significant technical challenge for research on mechanisms that drive metabolism, growth and development in roots, as well as on inter-organismal networks in the rhizosphere. Synthetic environments, combining microscopic access and manipulation capabilities with soil-like heterogeneity, are needed to elucidate the intriguing tug-of-war that characterises subsurface ecosystems. Microdevices have provided opportunities for innovative approaches to observe, analyse and manipulate plant roots and advanced our understanding of their development, physiology and interactions with the environment. Initially conceived as perfusion platforms for root cultivation under hydroponic conditions, microdevice design has, in recent years, increasingly shifted to better reflect the complex growth conditions in soil. Heterogeneous micro-environments have been created through co-cultivation with microbes, laminar flow-based local stimulation and physical obstacles and constraints. As such, structured microdevices provide an experimental entry point to the complex network behaviour of soil communities.
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Affiliation(s)
- Christian-Frederic Kaiser
- Institute of Cell and Interaction Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
- CEPLAS - Cluster of Excellence on Plant Sciences, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Alessia Perilli
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Guido Grossmann
- Institute of Cell and Interaction Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
- CEPLAS - Cluster of Excellence on Plant Sciences, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Yasmine Meroz
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
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6
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Pereira D, Alline T, Singh G, Chabouté ME, Asnacios A. A Microfluidic-Like System (MLS) to Grow, Image, and Quantitatively Characterize Rigidity Sensing by Plant's Roots and Root Hair Cells. Methods Mol Biol 2023; 2600:121-131. [PMID: 36587094 DOI: 10.1007/978-1-0716-2851-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Plant's roots grow in soils of different rigidities. Understanding how the stiffness of the surrounding environment impacts growth and cell fate of roots and root hair cells is an important and open question. Here, we describe a simple method to setup a microfluidic-like system (MLS) to tackle this question. This system enables to grow plantlets during weeks in microfluidic chips filled with gels of controlled stiffness and to image them under a microscope from a few minutes up to a few days. Furthermore, MLS keeps the numerous benefits of microfluidic chips, such as high-resolution imaging, precise control of the geometry of growth, and standardization of the measurements. In sum, MLS enables one to quantitatively test, even on long time scales, the effect of the rigidity and the geometry of the environment on the growth of roots and root hair cells, including mechanotransduction to the nucleus.
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Affiliation(s)
- David Pereira
- Université Paris Cité, CNRS, Laboratoire Matière et Systèmes Complexes, UMR 7057, Paris, France.
| | - Thomas Alline
- Université Paris Cité, CNRS, Laboratoire Matière et Systèmes Complexes, UMR 7057, Paris, France
| | - Gaurav Singh
- Institut de biologie moléculaire des plantes, UPR2357 CNRS, Université de Strasbourg, Strasbourg, France
| | - Marie-Edith Chabouté
- Institut de biologie moléculaire des plantes, UPR2357 CNRS, Université de Strasbourg, Strasbourg, France
| | - Atef Asnacios
- Université Paris Cité, CNRS, Laboratoire Matière et Systèmes Complexes, UMR 7057, Paris, France.
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7
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Hsiao AS, Huang JY. Bioimaging tools move plant physiology studies forward. FRONTIERS IN PLANT SCIENCE 2022; 13:976627. [PMID: 36204075 PMCID: PMC9530904 DOI: 10.3389/fpls.2022.976627] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Affiliation(s)
- An-Shan Hsiao
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Ji-Ying Huang
- Cell Biology Core Lab, Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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8
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Ranjbaran M, Verma MS. Microfluidics at the interface of bacteria and fresh produce. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.07.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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9
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Suwanchaikasem P, Idnurm A, Selby-Pham J, Walker R, Boughton BA. Root-TRAPR: a modular plant growth device to visualize root development and monitor growth parameters, as applied to an elicitor response of Cannabis sativa. PLANT METHODS 2022; 18:46. [PMID: 35397608 PMCID: PMC8994333 DOI: 10.1186/s13007-022-00875-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 03/14/2022] [Indexed: 05/08/2023]
Abstract
BACKGROUND Plant growth devices, for example, rhizoponics, rhizoboxes, and ecosystem fabrication (EcoFAB), have been developed to facilitate studies of plant root morphology and plant-microbe interactions in controlled laboratory settings. However, several of these designs are suitable only for studying small model plants such as Arabidopsis thaliana and Brachypodium distachyon and therefore require modification to be extended to larger plant species like crop plants. In addition, specific tools and technical skills needed for fabricating these devices may not be available to researchers. Hence, this study aimed to establish an alternative protocol to generate a larger, modular and reusable plant growth device based on different available resources. RESULTS Root-TRAPR (Root-Transparent, Reusable, Affordable three-dimensional Printed Rhizo-hydroponic) system was successfully developed. It consists of two main parts, an internal root growth chamber and an external structural frame. The internal root growth chamber comprises a polydimethylsiloxane (PDMS) gasket, microscope slide and acrylic sheet, while the external frame is printed from a three-dimensional (3D) printer and secured with nylon screws. To test the efficiency and applicability of the system, industrial hemp (Cannabis sativa) was grown with or without exposure to chitosan, a well-known plant elicitor used for stimulating plant defense. Plant root morphology was detected in the system, and plant tissues were easily collected and processed to examine plant biological responses. Upon chitosan treatment, chitinase and peroxidase activities increased in root tissues (1.7- and 2.3-fold, respectively) and exudates (7.2- and 21.6-fold, respectively). In addition, root to shoot ratio of phytohormone contents were increased in response to chitosan. Within 2 weeks of observation, hemp plants exhibited dwarf growth in the Root-TRAPR system, easing plant handling and allowing increased replication under limited growing space. CONCLUSION The Root-TRAPR system facilitates the exploration of root morphology and root exudate of C. sativa under controlled conditions and at a smaller scale. The device is easy to fabricate and applicable for investigating plant responses toward elicitor challenge. In addition, this fabrication protocol is adaptable to study other plants and can be applied to investigate plant physiology in different biological contexts, such as plant responses against biotic and abiotic stresses.
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Affiliation(s)
| | - Alexander Idnurm
- School of BioSciences, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Jamie Selby-Pham
- School of BioSciences, University of Melbourne, Melbourne, VIC, 3010, Australia
- Nutrifield Pty Ltd, Melbourne, VIC, 3020, Australia
| | - Robert Walker
- School of BioSciences, University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Berin A Boughton
- School of BioSciences, University of Melbourne, Melbourne, VIC, 3010, Australia
- Australian National Phenome Centre, Murdoch University, Perth, WA, 6150, Australia
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10
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Yanagisawa N, Kozgunova E, Grossmann G, Geitmann A, Higashiyama T. Microfluidics-Based Bioassays and Imaging of Plant Cells. PLANT & CELL PHYSIOLOGY 2021; 62:1239-1250. [PMID: 34027549 PMCID: PMC8579190 DOI: 10.1093/pcp/pcab067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/13/2021] [Accepted: 05/23/2021] [Indexed: 05/03/2023]
Abstract
Many plant processes occur in the context of and in interaction with a surrounding matrix such as soil (e.g. root growth and root-microbe interactions) or surrounding tissues (e.g. pollen tube growth through the pistil), making it difficult to study them with high-resolution optical microscopy. Over the past decade, microfabrication techniques have been developed to produce experimental systems that allow researchers to examine cell behavior in microstructured environments that mimic geometrical, physical and/or chemical aspects of the natural growth matrices and that cannot be generated using traditional agar plate assays. These microfabricated environments offer considerable design flexibility as well as the transparency required for high-resolution, light-based microscopy. In addition, microfluidic platforms have been used for various types of bioassays, including cellular force assays, chemoattraction assays and electrotropism assays. Here, we review the recent use of microfluidic devices to study plant cells and organs, including plant roots, root hairs, moss protonemata and pollen tubes. The increasing adoption of microfabrication techniques by the plant science community may transform our approaches to investigating how individual plant cells sense and respond to changes in the physical and chemical environment.
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Affiliation(s)
- Naoki Yanagisawa
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Nagoya Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Elena Kozgunova
- Department of Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Schänzlestr. 1, Freiburg, Baden-Württemberg 79104, Germany
| | - Guido Grossmann
- Institute of Cell and Interaction Biology, Heinrich Heine University Düsseldorf, Universitätsstr. 1, Düsseldorf 40225, Germany
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Baden-Württemberg 69120, Germany
| | - Anja Geitmann
- Department of Plant Science, Faculty of Agricultural and Environmental Sciences, McGill University, Québec H9X 3V9, Canada
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Nagoya Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo City, Tokyo 113-0033, Japan
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11
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Abstract
Collecting real-time data on physical and chemical parameters of the soil is a prerequisite for resource-efficient and environmentally sustainable agriculture. For continuous in situ measurement of soil nutrients such as nitrate or phosphate, a lab-on-chip approach combined with wireless remote readout is promising. For this purpose, the soil solution, i.e., the water in the soil with nutrients, needs to be extracted into a microfluidic chip. Here, we present a soil-solution extraction unit based on combining a porous ceramic filter with a microfluidic channel with a 12 µL volume. The microfluidic chip was fabricated from polydimethylsiloxane, had a size of 1.7 cm × 1.7 cm × 0.6 cm, and was bonded to a glass substrate. A hydrophilic aluminum oxide ceramic with approximately 37 Vol.-% porosity and an average pore size of 1 µm was integrated at the inlet. Soil water was extracted successfully from three types of soil—silt, garden soil, and sand—by creating suction with a pump at the other end of the microfluidic channel. For garden soil, the extraction rate at approximately 15 Vol.-% soil moisture was 1.4 µL/min. The amount of extracted water was investigated for 30 min pump intervals for the three soil types at different moisture levels. For garden soil and sand, water extraction started at around 10 Vol.-% soil moisture. Silt showed the highest water-holding capacity, with water extraction starting at approximately 13 Vol.-%.
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12
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Singh G, Pereira D, Baudrey S, Hoffmann E, Ryckelynck M, Asnacios A, Chabouté ME. Real-time tracking of root hair nucleus morphodynamics using a microfluidic approach. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:303-313. [PMID: 34562320 DOI: 10.1111/tpj.15511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 09/06/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Root hairs (RHs) are tubular extensions of root epidermal cells that favour nutrient uptake and microbe interactions. RHs show a fast apical growth, constituting a unique single cell model system for analysing cellular morphodynamics. In this context, live cell imaging using microfluidics recently developed to analyze root development is appealing, although high-resolution imaging is still lacking to enable an investigation of the accurate spatiotemporal morphodynamics of organelles. Here, we provide a powerful coverslip based microfluidic device (CMD) that enables us to capture high resolution confocal imaging of Arabidopsis RH development with real-time monitoring of nuclear movement and shape changes. To validate the setup, we confirmed the typical RH growth rates and the mean nuclear positioning previously reported with classical methods. Moreover, to illustrate the possibilities offered by the CMD, we have compared the real-time variations in the circularity, area and aspect ratio of nuclei moving in growing and mature RHs. Interestingly, we observed higher aspect ratios in the nuclei of mature RHs, correlating with higher speeds of nuclear migration. This observation opens the way for further investigations of the effect of mechanical constraints on nuclear shape changes during RH growth and nuclear migration and its role in RH and plant development.
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Affiliation(s)
- Gaurav Singh
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, 67084, France
| | - David Pereira
- Laboratoire Matière et Systèmes Complexes, UMR 7057, CNRS et Université de Paris, Paris, 75013, France
| | - Stéphanie Baudrey
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, 67000, France
| | - Elise Hoffmann
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, 67084, France
| | - Michael Ryckelynck
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, 67000, France
| | - Atef Asnacios
- Laboratoire Matière et Systèmes Complexes, UMR 7057, CNRS et Université de Paris, Paris, 75013, France
| | - Marie-Edith Chabouté
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, 67084, France
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13
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Sun Y, Tayagui A, Sale S, Sarkar D, Nock V, Garrill A. Platforms for High-Throughput Screening and Force Measurements on Fungi and Oomycetes. MICROMACHINES 2021; 12:mi12060639. [PMID: 34070887 PMCID: PMC8227076 DOI: 10.3390/mi12060639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 01/19/2023]
Abstract
Pathogenic fungi and oomycetes give rise to a significant number of animal and plant diseases. While the spread of these pathogenic microorganisms is increasing globally, emerging resistance to antifungal drugs is making associated diseases more difficult to treat. High-throughput screening (HTS) and new developments in lab-on-a-chip (LOC) platforms promise to aid the discovery of urgently required new control strategies and anti-fungal/oomycete drugs. In this review, we summarize existing HTS and emergent LOC approaches in the context of infection strategies and invasive growth exhibited by these microorganisms. To aid this, we introduce key biological aspects and review existing HTS platforms based on both conventional and LOC techniques. We then provide an in-depth discussion of more specialized LOC platforms for force measurements on hyphae and to study electro- and chemotaxis in spores, approaches which have the potential to aid the discovery of alternative drug targets on future HTS platforms. Finally, we conclude with a brief discussion of the technical developments required to improve the uptake of these platforms into the general laboratory environment.
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Affiliation(s)
- Yiling Sun
- Biomolecular Interaction Centre, Department of Electrical and Computer Engineering, University of Canterbury, Christchurch 8041, New Zealand; (Y.S.); (A.T.); (S.S.); (D.S.)
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington 6140, New Zealand
| | - Ayelen Tayagui
- Biomolecular Interaction Centre, Department of Electrical and Computer Engineering, University of Canterbury, Christchurch 8041, New Zealand; (Y.S.); (A.T.); (S.S.); (D.S.)
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington 6140, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch 8041, New Zealand
| | - Sarah Sale
- Biomolecular Interaction Centre, Department of Electrical and Computer Engineering, University of Canterbury, Christchurch 8041, New Zealand; (Y.S.); (A.T.); (S.S.); (D.S.)
- School of Biological Sciences, University of Canterbury, Christchurch 8041, New Zealand
| | - Debolina Sarkar
- Biomolecular Interaction Centre, Department of Electrical and Computer Engineering, University of Canterbury, Christchurch 8041, New Zealand; (Y.S.); (A.T.); (S.S.); (D.S.)
- School of Biological Sciences, University of Canterbury, Christchurch 8041, New Zealand
| | - Volker Nock
- Biomolecular Interaction Centre, Department of Electrical and Computer Engineering, University of Canterbury, Christchurch 8041, New Zealand; (Y.S.); (A.T.); (S.S.); (D.S.)
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington 6140, New Zealand
- Correspondence: (V.N.); (A.G.)
| | - Ashley Garrill
- Biomolecular Interaction Centre, Department of Electrical and Computer Engineering, University of Canterbury, Christchurch 8041, New Zealand; (Y.S.); (A.T.); (S.S.); (D.S.)
- School of Biological Sciences, University of Canterbury, Christchurch 8041, New Zealand
- Correspondence: (V.N.); (A.G.)
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14
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Yee MO, Kim P, Li Y, Singh AK, Northen TR, Chakraborty R. Specialized Plant Growth Chamber Designs to Study Complex Rhizosphere Interactions. Front Microbiol 2021; 12:625752. [PMID: 33841353 PMCID: PMC8032546 DOI: 10.3389/fmicb.2021.625752] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/19/2021] [Indexed: 01/19/2023] Open
Abstract
The rhizosphere is a dynamic ecosystem shaped by complex interactions between plant roots, soil, microbial communities and other micro- and macro-fauna. Although studied for decades, critical gaps exist in the study of plant roots, the rhizosphere microbiome and the soil system surrounding roots, partly due to the challenges associated with measuring and parsing these spatiotemporal interactions in complex heterogeneous systems such as soil. To overcome the challenges associated with in situ study of rhizosphere interactions, specialized plant growth chamber systems have been developed that mimic the natural growth environment. This review discusses the currently available lab-based systems ranging from widely known rhizotrons to other emerging devices designed to allow continuous monitoring and non-destructive sampling of the rhizosphere ecosystems in real-time throughout the developmental stages of a plant. We categorize them based on the major rhizosphere processes it addresses and identify their unique challenges as well as advantages. We find that while some design elements are shared among different systems (e.g., size exclusion membranes), most of the systems are bespoke and speaks to the intricacies and specialization involved in unraveling the details of rhizosphere processes. We also discuss what we describe as the next generation of growth chamber employing the latest technology as well as the current barriers they face. We conclude with a perspective on the current knowledge gaps in the rhizosphere which can be filled by innovative chamber designs.
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Affiliation(s)
- Mon Oo Yee
- Climate and Ecosystem Sciences, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Peter Kim
- CBRN Defense and Energy Technologies, Sandia National Laboratories, Livermore, CA, United States
| | - Yifan Li
- Climate and Ecosystem Sciences, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Anup K. Singh
- CBRN Defense and Energy Technologies, Sandia National Laboratories, Livermore, CA, United States
| | - Trent R. Northen
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Romy Chakraborty
- Climate and Ecosystem Sciences, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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15
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Ke J, Wang B, Yoshikuni Y. Microbiome Engineering: Synthetic Biology of Plant-Associated Microbiomes in Sustainable Agriculture. Trends Biotechnol 2020; 39:244-261. [PMID: 32800605 DOI: 10.1016/j.tibtech.2020.07.008] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 12/28/2022]
Abstract
To support an ever-increasing population, modern agriculture faces numerous challenges that pose major threats to global food and energy security. Plant-associated microbes, with their many plant growth-promoting (PGP) traits, have enormous potential in helping to solve these challenges. However, the results of their use in agriculture have been variable, probably because of poor colonization. Phytomicrobiome engineering is an emerging field of synthetic biology that may offer ways to alleviate this limitation. This review highlights recent advances in both bottom-up and top-down approaches to engineering non-model bacteria and microbiomes to promote beneficial plant-microbe interactions, as well as advances in strategies to evaluate these interactions. Biosafety, biosecurity, and biocontainment strategies to address the environmental concerns associated with field use of synthetic microbes are also discussed.
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Affiliation(s)
- Jing Ke
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Bing Wang
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yasuo Yoshikuni
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Center for Advanced Bioenergy and Bioproducts Innovation, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Global Institution for Collaborative Research and Education, Hokkaido University, Hokkaido 060-8589, Japan.
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16
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Guichard M, Bertran Garcia de Olalla E, Stanley CE, Grossmann G. Microfluidic systems for plant root imaging. Methods Cell Biol 2020; 160:381-404. [PMID: 32896330 DOI: 10.1016/bs.mcb.2020.03.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Plant roots adapt their development and metabolism to changing environmental conditions. In order to understand the response mechanisms of roots to the dynamic availability of water or nutrients, to biotic and abiotic stress conditions or to mechanical stimuli, microfluidic platforms have been developed that offer microscopic access and novel experimental means. Here, we describe the design, fabrication and use of microfluidic devices suitable for imaging growing Arabidopsis roots over several days under controlled perfusion. We present a detailed protocol for the use of our exemplar platform-the RootChip-8S-and offer a guide for troubleshooting, which is also largely applicable to related device designs. We further discuss considerations regarding the design of custom-made plant microdevices, the choice of suitable materials and technologies as well as the handling of the specimen.
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Affiliation(s)
- Marjorie Guichard
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | | | | | - Guido Grossmann
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany,; Excellence Cluster CellNetworks, Heidelberg University, Heidelberg, Germany,.
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17
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Sasse J, Kosina SM, de Raad M, Jordan JS, Whiting K, Zhalnina K, Northen TR. Root morphology and exudate availability are shaped by particle size and chemistry in Brachypodium distachyon. PLANT DIRECT 2020; 4:e00207. [PMID: 32642632 PMCID: PMC7330624 DOI: 10.1002/pld3.207] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 02/04/2020] [Accepted: 02/11/2020] [Indexed: 05/26/2023]
Abstract
Root morphology and exudation define a plants' sphere of influence in soils. In turn, soil characteristics influence plant growth, morphology, root microbiome, and rhizosphere chemistry. Collectively, all these parameters have significant implications on the major biogeochemical cycles, crop yield, and ecosystem health. However, how plants are shaped by the physiochemistry of soil particles is still not well understood. We explored how particle size and chemistry of growth substrates affect root morphology and exudation of a model grass. We grew Brachypodium distachyon in glass beads with various sizes (0.5, 1, 2, 3 mm), as well as in sand (0.005, 0.25, 4 mm) and in clay (4 mm) particles and in particle-free hydroponic medium. Plant morphology, root weight, and shoot weight were measured. We found that particle size significantly influenced root fresh weight and root length, whereas root number and shoot weight remained constant. Next, plant exudation profiles were analyzed with mass spectrometry imaging and liquid chromatography-mass spectrometry. Mass spectrometry imaging suggested that both, root length and number shape root exudation. Exudate profiles were comparable for plants growing in glass beads or sand with various particles sizes, but distinct for plants growing in clay for in situ exudate collection. Clay particles were found to sorb 20% of compounds exuded by clay-grown plants, and 70% of compounds from a defined exudate medium. The sorbed compounds belonged to a range of chemical classes, among them nucleosides, organic acids, sugars, and amino acids. Some of the sorbed compounds could be desorbed by a rhizobacterium (Pseudomonas fluorescens WCS415), supporting its growth. This study demonstrates the effect of different characteristics of particles on root morphology, plant exudation and availability of nutrients to microorganisms. These findings further support the critical importance of the physiochemical properties of soils when investigating plant morphology, plant chemistry, and plant-microbe interactions.
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Affiliation(s)
- Joelle Sasse
- Environmental Genomics and Systems BiologyLawrence Berkeley National LaboratoryBerkeleyCAUSA
- Department of Plant and Microbial BiologyUniversity of ZurichZurichSwitzerland
| | - Suzanne M. Kosina
- Environmental Genomics and Systems BiologyLawrence Berkeley National LaboratoryBerkeleyCAUSA
| | - Markus de Raad
- Environmental Genomics and Systems BiologyLawrence Berkeley National LaboratoryBerkeleyCAUSA
| | - Jacob S. Jordan
- Environmental Genomics and Systems BiologyLawrence Berkeley National LaboratoryBerkeleyCAUSA
- Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCAUSA
| | - Katherine Whiting
- Environmental Genomics and Systems BiologyLawrence Berkeley National LaboratoryBerkeleyCAUSA
| | - Kateryna Zhalnina
- Environmental Genomics and Systems BiologyLawrence Berkeley National LaboratoryBerkeleyCAUSA
| | - Trent R. Northen
- Environmental Genomics and Systems BiologyLawrence Berkeley National LaboratoryBerkeleyCAUSA
- Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCAUSA
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18
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Clark NM, Van den Broeck L, Guichard M, Stager A, Tanner HG, Blilou I, Grossmann G, Iyer-Pascuzzi AS, Maizel A, Sparks EE, Sozzani R. Novel Imaging Modalities Shedding Light on Plant Biology: Start Small and Grow Big. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:789-816. [PMID: 32119794 DOI: 10.1146/annurev-arplant-050718-100038] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The acquisition of quantitative information on plant development across a range of temporal and spatial scales is essential to understand the mechanisms of plant growth. Recent years have shown the emergence of imaging methodologies that enable the capture and analysis of plant growth, from the dynamics of molecules within cells to the measurement of morphometricand physiological traits in field-grown plants. In some instances, these imaging methods can be parallelized across multiple samples to increase throughput. When high throughput is combined with high temporal and spatial resolution, the resulting image-derived data sets could be combined with molecular large-scale data sets to enable unprecedented systems-level computational modeling. Such image-driven functional genomics studies may be expected to appear at an accelerating rate in the near future given the early success of the foundational efforts reviewed here. We present new imaging modalities and review how they have enabled a better understanding of plant growth from the microscopic to the macroscopic scale.
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Affiliation(s)
- Natalie M Clark
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695, USA; ,
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50010, USA;
| | - Lisa Van den Broeck
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695, USA; ,
| | - Marjorie Guichard
- Center for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany; , ,
- CellNetworks Cluster of Excellence, Heidelberg University, 69120 Heidelberg, Germany
| | - Adam Stager
- Department of Mechanical Engineering, University of Delaware, Newark, Delaware 19711, USA; ,
| | - Herbert G Tanner
- Department of Mechanical Engineering, University of Delaware, Newark, Delaware 19711, USA; ,
| | - Ikram Blilou
- Department of Plant Cell and Developmental Biology, Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia;
| | - Guido Grossmann
- Center for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany; , ,
- CellNetworks Cluster of Excellence, Heidelberg University, 69120 Heidelberg, Germany
| | - Anjali S Iyer-Pascuzzi
- Department of Botany and Plant Pathology and Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA;
| | - Alexis Maizel
- Center for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany; , ,
| | - Erin E Sparks
- Department of Plant and Soil Sciences and the Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA;
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695, USA; ,
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19
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Noirot-Gros MF, Shinde SV, Akins C, Johnson JL, Zerbs S, Wilton R, Kemner KM, Noirot P, Babnigg G. Functional Imaging of Microbial Interactions With Tree Roots Using a Microfluidics Setup. FRONTIERS IN PLANT SCIENCE 2020; 11:408. [PMID: 32351525 PMCID: PMC7174594 DOI: 10.3389/fpls.2020.00408] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 03/20/2020] [Indexed: 05/20/2023]
Abstract
Coupling microfluidics with microscopy has emerged as a powerful approach to study at cellular resolution the dynamics in plant physiology and root-microbe interactions (RMIs). Most devices have been designed to study the model plant Arabidopsis thaliana at higher throughput than conventional methods. However, there is a need for microfluidic devices which enable in vivo studies of root development and RMIs in woody plants. Here, we developed the RMI-chip, a simple microfluidic setup in which Populus tremuloides (aspen tree) seedlings can grow for over a month, allowing continuous microscopic observation of interactions between live roots and rhizobacteria. We find that the colonization of growing aspen roots by Pseudomonas fluorescens in the RMI-chip involves dynamic biofilm formation and dispersal, in keeping with previous observations in a different experimental set-up. Also, we find that whole-cell biosensors based on the rhizobacterium Bacillus subtilis can be used to monitor compositional changes in the rhizosphere but that the application of these biosensors is limited by their efficiency at colonizing aspen roots and persisting. These results indicate that functional imaging of dynamic root-bacteria interactions in the RMI-chip requires careful matching between the host plant and the bacterial root colonizer.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Gyorgy Babnigg
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
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20
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Park YH, Park JK. Light Gradient-Based Screening of Arabidopsis thaliana on a 384-Well Type Plant Array Chip. MICROMACHINES 2020; 11:E191. [PMID: 32059534 PMCID: PMC7074641 DOI: 10.3390/mi11020191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/07/2020] [Accepted: 02/08/2020] [Indexed: 12/03/2022]
Abstract
Arabidopsis thaliana (Arabidopsis), as a model for plant research, is widely used for various aspects of plant science. To provide a more sophisticated and microscopic environment for the germination and growth of Arabidopsis, we report a 384-well type plant array chip in which each Arabidopsis seed is independently seeded in a solid medium. The plant array chip is made of a poly(methyl methacrylate) (PMMA) acrylic material and is assembled with a home-made light gradient module to investigate the light effects that significantly affect the germination and growth of Arabidopsis. The light gradient module was used to observe the growth pattern of seedlings according to the intensity of the white light and to efficiently screen for the influence of the white light. To investigate the response to red light (600 nm), which stimulates seed germination, the light gradient module was also applied to the germination test. As a result, the germination results showed that the plant array chip can be used to simultaneously screen wild type seeds and phytochrome B mutant seeds on a single array chip according to the eight red light intensities.
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Affiliation(s)
- Youn-Hee Park
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea;
| | - Je-Kyun Park
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea;
- KAIST Institute for Health Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
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21
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Horowitz LF, Rodriguez AD, Ray T, Folch A. Microfluidics for interrogating live intact tissues. MICROSYSTEMS & NANOENGINEERING 2020; 6:69. [PMID: 32879734 PMCID: PMC7443437 DOI: 10.1038/s41378-020-0164-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 03/10/2020] [Accepted: 03/12/2020] [Indexed: 05/08/2023]
Abstract
The intricate microarchitecture of tissues - the "tissue microenvironment" - is a strong determinant of tissue function. Microfluidics offers an invaluable tool to precisely stimulate, manipulate, and analyze the tissue microenvironment in live tissues and engineer mass transport around and into small tissue volumes. Such control is critical in clinical studies, especially where tissue samples are scarce, in analytical sensors, where testing smaller amounts of analytes results in faster, more portable sensors, and in biological experiments, where accurate control of the cellular microenvironment is needed. Microfluidics also provides inexpensive multiplexing strategies to address the pressing need to test large quantities of drugs and reagents on a single biopsy specimen, increasing testing accuracy, relevance, and speed while reducing overall diagnostic cost. Here, we review the use of microfluidics to study the physiology and pathophysiology of intact live tissues at sub-millimeter scales. We categorize uses as either in vitro studies - where a piece of an organism must be excised and introduced into the microfluidic device - or in vivo studies - where whole organisms are small enough to be introduced into microchannels or where a microfluidic device is interfaced with a live tissue surface (e.g. the skin or inside an internal organ or tumor) that forms part of an animal larger than the device. These microfluidic systems promise to deliver functional measurements obtained directly on intact tissue - such as the response of tissue to drugs or the analysis of tissue secretions - that cannot be obtained otherwise.
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Affiliation(s)
- Lisa F. Horowitz
- Department of Bioengineering, University of Washington, Seattle, WA 98195 USA
| | - Adán D. Rodriguez
- Department of Bioengineering, University of Washington, Seattle, WA 98195 USA
| | - Tyler Ray
- Department of Mechanical Engineering, University of Hawaiʻi at Mānoa, Honolulu, HI 96822 USA
| | - Albert Folch
- Department of Bioengineering, University of Washington, Seattle, WA 98195 USA
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22
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A Foldable Chip Array for the Continuous Investigation of Seed Germination and the Subsequent Root Development of Seedlings. MICROMACHINES 2019; 10:mi10120884. [PMID: 31861063 PMCID: PMC6953092 DOI: 10.3390/mi10120884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/08/2019] [Accepted: 12/13/2019] [Indexed: 11/29/2022]
Abstract
Seed germination and seedling root development are important indicators of plant development. This work designed and fabricated a foldable microfluidic chip array for conducting nondestructive and continuous evaluation of seed germination and subsequent seedling development in situ. Each plant chamber has two functional units: seed germination part and root-growth part. The root-growth parts are themselves connected to a single channel designed to provide a uniform culture medium for plant growth. The individual chips are connected into an array using elastic hinges that facilitate the folding and unfolding of the array to accommodate different viewing purposes. In the folded state, the seed germination chambers form a closely spaced array platform to facilitate the comparison of seed germination and plant development characteristics. Unfolding the array facilitates a clear examination of root development within the root-growth parts. The observation window of an individual chip facilitates either the direct examination of the developing seedling (e.g., stems and leaves) or the use of a microscope for examining microscale features (e.g., root tips and root hairs). The potential of the proposed foldable chip array as a new cultivation platform for botanic studies is demonstrated by examining the seed germination and seedling development of tobacco (Nicotiana tabacum) under different cultivation conditions.
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23
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Chai HH, Chen F, Zhang SJ, Li YD, Lu ZS, Kang YJ, Yu L. Multi-chamber petaloid root-growth chip for the non-destructive study of the development and physiology of the fibrous root system of Oryza sativa. LAB ON A CHIP 2019; 19:2383-2393. [PMID: 31187104 DOI: 10.1039/c9lc00396g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The root system of plants is a major component of their bodies in terms of both function and bulk. The investigation of root system development is greatly assisted by microfluidic devices, which improve the spatial and temporal resolution of observations without destroying tissue. In the present study, a multi-chamber petaloid root-growth chip was developed for studying the development and physiology of root systems that have thin branching structures (i.e., fibrous root systems). The petaloid root-growth chip includes a central seed germination chamber and five root-growth chambers for observing the development of fibrous roots. The proposed device was applied for investigating the root system development of Oryza sativa. The phenotype and growth kinetics of O. sativa root systems grown in the proposed device were compared with those obtained during growth in a conventional conical flask with agar-based medium, and the results indicated that cultivation in the miniaturized device did not delay root system growth in the early stage (≤2 weeks). In addition, the transparent device enabled the non-destructive observation of the developmental and microstructural characteristics of the roots, such as the root caps, root border cells, and root hairs. Moreover, the ability to control the microenvironment in each of the five root-growth chambers individually facilitated the investigation of specific adaptations in the fibrous root growth of single O. sativa seedlings to different drought stresses. Accordingly, five polyethylene glycol (PEG)6000-induced drought stress conditions were established in the five root-growth chambers to investigate the root development of a single O. sativa seedling in the central germination chamber. In situ observations demonstrated that the different PEG6000-induced conditions affected the root growth responses and root microstructural adaptations of the single seedlings in each root-growth chamber. Therefore, the petaloid root-growth microfluidic chip can eliminate the effects of variations in different plant seeds to reveal the responses of plants to different environmental conditions more objectively while concurrently allowing for non-destructive observations at very high spatial and temporal resolution.
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Affiliation(s)
- Hui Hui Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, Institute for Clean Energy and Advanced Materials, Faculty of Materials and Energy, Southwest University, Chongqing 400715, PR China.
| | - Feng Chen
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, Institute for Clean Energy and Advanced Materials, Faculty of Materials and Energy, Southwest University, Chongqing 400715, PR China.
| | - Shu Jie Zhang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, Institute for Clean Energy and Advanced Materials, Faculty of Materials and Energy, Southwest University, Chongqing 400715, PR China.
| | - Ya Dan Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, Institute for Clean Energy and Advanced Materials, Faculty of Materials and Energy, Southwest University, Chongqing 400715, PR China.
| | - Zhi Song Lu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, Institute for Clean Energy and Advanced Materials, Faculty of Materials and Energy, Southwest University, Chongqing 400715, PR China.
| | - Yue Jun Kang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, Institute for Clean Energy and Advanced Materials, Faculty of Materials and Energy, Southwest University, Chongqing 400715, PR China.
| | - Ling Yu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, Institute for Clean Energy and Advanced Materials, Faculty of Materials and Energy, Southwest University, Chongqing 400715, PR China. and Guangan Changming Research Institute for Advanced Industrial Technology, Guangan 638500, PR China
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24
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Sasse J, Kant J, Cole BJ, Klein AP, Arsova B, Schlaepfer P, Gao J, Lewald K, Zhalnina K, Kosina S, Bowen BP, Treen D, Vogel J, Visel A, Watt M, Dangl JL, Northen TR. Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass. THE NEW PHYTOLOGIST 2019; 222:1149-1160. [PMID: 30585637 PMCID: PMC6519027 DOI: 10.1111/nph.15662] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/18/2018] [Indexed: 05/12/2023]
Abstract
There is a dynamic reciprocity between plants and their environment: soil physiochemical properties influence plant morphology and metabolism, and root morphology and exudates shape the environment surrounding roots. Here, we investigate the reproducibility of plant trait changes in response to three growth environments. We utilized fabricated ecosystem (EcoFAB) devices to grow the model grass Brachypodium distachyon in three distinct media across four laboratories: phosphate-sufficient and -deficient mineral media allowed assessment of the effects of phosphate starvation, and a complex, sterile soil extract represented a more natural environment with yet uncharacterized effects on plant growth and metabolism. Tissue weight and phosphate content, total root length, and root tissue and exudate metabolic profiles were consistent across laboratories and distinct between experimental treatments. Plants grown in soil extract were morphologically and metabolically distinct, with root hairs four times longer than with other growth conditions. Further, plants depleted half of the metabolites investigated from the soil extract. To interact with their environment, plants not only adapt morphology and release complex metabolite mixtures, but also selectively deplete a range of soil-derived metabolites. The EcoFABs utilized here generated high interlaboratory reproducibility, demonstrating their value in standardized investigations of plant traits.
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Affiliation(s)
- Joelle Sasse
- Lawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
- Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
| | - Josefine Kant
- Institut für Bio‐ & GeowissenschaftenForschungszentrum JülichWilhelm‐Johnen‐Straße52428JülichGermany
| | - Benjamin J. Cole
- Lawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
- Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
| | - Andrew P. Klein
- Department of BiologyHoward Hughes Medical InstituteUniversity of North Carolina Chapel Hill250 Bell Tower DriveChapel HillNC27599USA
| | - Borjana Arsova
- Institut für Bio‐ & GeowissenschaftenForschungszentrum JülichWilhelm‐Johnen‐Straße52428JülichGermany
| | - Pascal Schlaepfer
- Institute of Molecular Plant BiologyETH ZürichUniversitätsstrasse 28092ZürichSwitzerland
| | - Jian Gao
- Lawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
- Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
| | - Kyle Lewald
- Lawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
- Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
| | - Kateryna Zhalnina
- Lawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
- Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
| | - Suzanne Kosina
- Lawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
- Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
| | - Benjamin P. Bowen
- Lawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
- Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
| | - Daniel Treen
- Lawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
- Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
| | - John Vogel
- Lawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
- Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
| | - Axel Visel
- Lawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
- Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
- School of Natural SciencesUniversity of CaliforniaMercedCA95343USA
| | - Michelle Watt
- Institut für Bio‐ & GeowissenschaftenForschungszentrum JülichWilhelm‐Johnen‐Straße52428JülichGermany
| | - Jeffery L. Dangl
- Department of BiologyHoward Hughes Medical InstituteUniversity of North Carolina Chapel Hill250 Bell Tower DriveChapel HillNC27599USA
| | - Trent R. Northen
- Lawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
- Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
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25
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Stanley CE, Shrivastava J, Brugman R, Heinzelmann E, Frajs V, Bühler A, van Swaay D, Grossmann G. Fabrication and use of the dual-flow-RootChip for the imaging of Arabidopsis roots in asymmetric microenvironments. Bio Protoc 2018; 8:e3010. [PMID: 34395800 DOI: 10.21769/bioprotoc.3010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/20/2018] [Accepted: 09/04/2018] [Indexed: 11/02/2022] Open
Abstract
This protocol provides a detailed description of how to fabricate and use the dual-flow-RootChip (dfRootChip), a novel microfluidic platform for investigating root nutrition, root-microbe interactions and signaling and development in controlled asymmetric conditions. The dfRootChip was developed primarily to investigate how plants roots interact with their environment by simulating environmental heterogeneity. The goal of this protocol is to provide a detailed resource for researchers in the biological sciences wishing to employ the dfRootChip in particular, or microfluidic devices in general, in their laboratory.
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Affiliation(s)
- Claire E Stanley
- Agroecology and Environment Research Division, Agroscope, Zürich, Switzerland
| | - Jagriti Shrivastava
- Centre for Organismal Studies (COS) Heidelberg, Universität Heidelberg, Heidelberg, Germany.,Heidelberg Biosciences International Graduate School of Heidelberg Molecular Life Sciences (HBIGS), Universität Heidelberg, Heidelberg, Germany
| | - Rik Brugman
- Centre for Organismal Studies (COS) Heidelberg, Universität Heidelberg, Heidelberg, Germany
| | - Elisa Heinzelmann
- Centre for Organismal Studies (COS) Heidelberg, Universität Heidelberg, Heidelberg, Germany
| | - Viktoria Frajs
- Centre for Organismal Studies (COS) Heidelberg, Universität Heidelberg, Heidelberg, Germany
| | - Andreas Bühler
- Agroecology and Environment Research Division, Agroscope, Zürich, Switzerland
| | - Dirk van Swaay
- Institute for Chemical and Bioengineering, ETH Zürich, Zürich, Switzerland
| | - Guido Grossmann
- Centre for Organismal Studies (COS) Heidelberg, Universität Heidelberg, Heidelberg, Germany.,CellNetworks-Cluster of Excellence, Universität Heidelberg, Heidelberg, Germany
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26
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Retterer ST, Morrell-Falvey JL, Doktycz MJ. Nano-Enabled Approaches to Chemical Imaging in Biosystems. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2018; 11:351-373. [PMID: 29490189 DOI: 10.1146/annurev-anchem-061417-125635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Understanding and predicting how biosystems function require knowledge about the dynamic physicochemical environments with which they interact and alter by their presence. Yet, identifying specific components, tracking the dynamics of the system, and monitoring local environmental conditions without disrupting biosystem function present significant challenges for analytical measurements. Nanomaterials, by their very size and nature, can act as probes and interfaces to biosystems and offer solutions to some of these challenges. At the nanoscale, material properties emerge that can be exploited for localizing biomolecules and making chemical measurements at cellular and subcellular scales. Here, we review advances in chemical imaging enabled by nanoscale structures, in the use of nanoparticles as chemical and environmental probes, and in the development of micro- and nanoscale fluidic devices to define and manipulate local environments and facilitate chemical measurements of complex biosystems. Integration of these nano-enabled methods will lead to an unprecedented understanding of biosystem function.
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Affiliation(s)
- Scott T Retterer
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA;
- Center for Nanophase Materials Science, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | | | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA;
- Center for Nanophase Materials Science, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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27
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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] [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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28
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Siemianowski O, Lind KR, Tian X, Cain M, Xu S, Ganapathysubramanian B, Cademartiri L. HOMEs for plants and microbes - a phenotyping approach with quantitative control of signaling between organisms and their individual environments. LAB ON A CHIP 2018; 18:620-626. [PMID: 29337318 DOI: 10.1039/c7lc01186e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We describe a simple, scalable, modular, and frugal approach to create model ecosystems as millifluidic networks of interconnected habitats (hosting microbes or plants), which offers (i) quantitative and dynamic control over the exchange of chemicals between habitats, and (ii) independent control over their environment. Oscillatory laminar flows produce regions of vortex mixing around obstacles. When these overlap, rapid mass transport by dispersion occurs, which is quantitatively describable as diffusion, but is directional and tunable in rate over 3 orders of magnitude. This acceleration in the rate of diffusion is equivalent to reducing the distance between the habitats, and therefore, the organisms, down to the length scales characteristic of signaling in soil (<2 mm).
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Affiliation(s)
- Oskar Siemianowski
- Department of Materials Science & Engineering, Iowa State University of Science and Technology, 2220 Hoover Hall, Ames, IA 50011, USA.
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29
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Stanley CE, Shrivastava J, Brugman R, Heinzelmann E, van Swaay D, Grossmann G. Dual-flow-RootChip reveals local adaptations of roots towards environmental asymmetry at the physiological and genetic levels. THE NEW PHYTOLOGIST 2018; 217:1357-1369. [PMID: 29125191 DOI: 10.1111/nph.14887] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 10/11/2017] [Indexed: 05/06/2023]
Abstract
Roots grow in highly dynamic and heterogeneous environments. Biological activity as well as uneven nutrient availability or localized stress factors result in diverse microenvironments. Plants adapt their root morphology in response to changing environmental conditions, yet it remains largely unknown to what extent developmental adaptations are based on systemic or cell-autonomous responses. We present the dual-flow-RootChip, a microfluidic platform for asymmetric perfusion of Arabidopsis roots to investigate root-environment interactions under simulated environmental heterogeneity. Applications range from investigating physiology, root hair development and calcium signalling upon selective exposure to environmental stresses to tracing molecular uptake, performing selective drug treatments and localized inoculations with microbes. Using the dual-flow-RootChip, we revealed cell-autonomous adaption of root hair development under asymmetric phosphate (Pi) perfusion, with unexpected repression in root hair growth on the side exposed to low Pi and rapid tip-growth upregulation when Pi concentrations increased. The asymmetric root environment further resulted in an asymmetric gene expression of RSL4, a key transcriptional regulator of root hair growth. Our findings demonstrate that roots possess the capability to locally adapt to heterogeneous conditions in their environment at the physiological and transcriptional levels. Being able to generate asymmetric microenvironments for roots will help further elucidate decision-making processes in root-environment interactions.
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Affiliation(s)
- Claire E Stanley
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland
- Agroecology and Environment Research Division, Agroscope, Reckenholzstrasse 191, 8046, Zürich, Switzerland
| | - Jagriti Shrivastava
- Centre for Organismal Studies (COS) Heidelberg, Universität Heidelberg, 69120, Heidelberg, Germany
- Hartmut Hoffmann-Berling International Graduate School of Heidelberg Molecular Life Sciences (HBIGS), Universität Heidelberg, 69120, Heidelberg, Germany
| | - Rik Brugman
- Centre for Organismal Studies (COS) Heidelberg, Universität Heidelberg, 69120, Heidelberg, Germany
| | - Elisa Heinzelmann
- Centre for Organismal Studies (COS) Heidelberg, Universität Heidelberg, 69120, Heidelberg, Germany
| | - Dirk van Swaay
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland
| | - Guido Grossmann
- Centre for Organismal Studies (COS) Heidelberg, Universität Heidelberg, 69120, Heidelberg, Germany
- CellNetworks-Cluster of Excellence, Universität Heidelberg, 69120, Heidelberg, Germany
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30
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Grossmann G, Krebs M, Maizel A, Stahl Y, Vermeer JEM, Ott T. Green light for quantitative live-cell imaging in plants. J Cell Sci 2018; 131:jcs.209270. [PMID: 29361538 DOI: 10.1242/jcs.209270] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Plants exhibit an intriguing morphological and physiological plasticity that enables them to thrive in a wide range of environments. To understand the cell biological basis of this unparalleled competence, a number of methodologies have been adapted or developed over the last decades that allow minimal or non-invasive live-cell imaging in the context of tissues. Combined with the ease to generate transgenic reporter lines in specific genetic backgrounds or accessions, we are witnessing a blooming in plant cell biology. However, the imaging of plant cells entails a number of specific challenges, such as high levels of autofluorescence, light scattering that is caused by cell walls and their sensitivity to environmental conditions. Quantitative live-cell imaging in plants therefore requires adapting or developing imaging techniques, as well as mounting and incubation systems, such as micro-fluidics. Here, we discuss some of these obstacles, and review a number of selected state-of-the-art techniques, such as two-photon imaging, light sheet microscopy and variable angle epifluorescence microscopy that allow high performance and minimal invasive live-cell imaging in plants.
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Affiliation(s)
- Guido Grossmann
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany.,Excellence Cluster CellNetworks, Heidelberg University, 69120 Heidelberg, Germany
| | - Melanie Krebs
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Alexis Maizel
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Yvonne Stahl
- Institute for Developmental Genetics, Heinrich-Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Joop E M Vermeer
- Laboratory for Cell Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Thomas Ott
- Faculty of Biology, Cell Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
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31
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Abstract
Plant roots play a dominant role in shaping the rhizosphere, the environment in which interaction with diverse microorganisms occurs. Tracking the dynamics of root-microbe interactions at high spatial resolution is currently limited because of methodological intricacy. Here, we describe a microfluidics-based approach enabling direct imaging of root-bacteria interactions in real time. The microfluidic device, which we termed tracking root interactions system (TRIS), consists of nine independent chambers that can be monitored in parallel. The principal assay reported here monitors behavior of fluorescently labeled Bacillus subtilis as it colonizes the root of Arabidopsis thaliana within the TRIS device. Our results show a distinct chemotactic behavior of B. subtilis toward a particular root segment, which we identify as the root elongation zone, followed by rapid colonization of that same segment over the first 6 h of root-bacteria interaction. Using dual inoculation experiments, we further show active exclusion of Escherichia coli cells from the root surface after B. subtilis colonization, suggesting a possible protection mechanism against root pathogens. Furthermore, we assembled a double-channel TRIS device that allows simultaneous tracking of two root systems in one chamber and performed real-time monitoring of bacterial preference between WT and mutant root genotypes. Thus, the TRIS microfluidics device provides unique insights into the microscale microbial ecology of the complex root microenvironment and is, therefore, likely to enhance the current rate of discoveries in this momentous field of research.
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32
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Abstract
The development of microfabricated devices that will provide high-throughput quantitative data and high resolution in a fast, repeatable and reproducible manner is essential for plant biology research.
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Affiliation(s)
- Meltem Elitaş
- Department of Mechatronics
- Faculty of Engineering and Natural Sciences
- Sabanci University
- 34956, Istanbul
- Turkey
| | - Meral Yüce
- Nanotechnology Research and Application Centre
- Sabanci University
- 34956, Istanbul
- Turkey
| | - Hikmet Budak
- Department of Molecular Biology
- Genetics and Bioengineering
- Faculty of Engineering and Natural Sciences
- Sabanci University
- 34956, Istanbul
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33
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Xu Z, Liu Q, Zhang X, Huang X, He P, Liu S, Sui G. A microfluidic chip for studying the reproduction of Enteromorpha prolifera. Talanta 2016; 160:577-585. [PMID: 27591653 DOI: 10.1016/j.talanta.2016.07.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 07/12/2016] [Accepted: 07/21/2016] [Indexed: 11/18/2022]
Abstract
In recent years, green tides caused by water eutrophication, has brought serious environmental problems. Enteromorpha prolifera (E. prolifera), an opportunistic macroalgae, is one of the main source contributing to the formation of green tides. It has been estimated that the excessive growth of E. prolifera is closely related to various reproductive ways of germ cells which are at the micrometer scale. Here we report a microfluidic device named Germ Cell Capture Chip (GCChip) to investigate the E. prolifera reproductive mechanism. GCChip integrates the functions of algal growing, and the release, capture and selective culture of germ cells. Automatic separation and capture of germ cells on the chip allows to study germ cells' response to different stimuli. The novel device greatly facilitates long-term live-cell imaging at cellular resolution and implements the rapid and accurate exchange of growth medium without manual intervention. Results showed that the starting time of germ cell releases were earlier on the chip than that of traditional experiments with more concentrated breakout. Moreover, GCChip can be widely applied on the study of other algae. The study of algae growth process, including the elongation of somatic cell, the generation, and the release of reproductive cells, can all be improved by using this microfluidic platform.
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Affiliation(s)
- Zhixuan Xu
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science & Engineering, Institute of Biomedical Science, Fudan University, Shanghai, China
| | - Qi Liu
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science & Engineering, Institute of Biomedical Science, Fudan University, Shanghai, China
| | - Xinlian Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science & Engineering, Institute of Biomedical Science, Fudan University, Shanghai, China
| | - Xuxiong Huang
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, PR China
| | - Peimin He
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, PR China
| | - Sixiu Liu
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science & Engineering, Institute of Biomedical Science, Fudan University, Shanghai, China
| | - Guodong Sui
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science & Engineering, Institute of Biomedical Science, Fudan University, Shanghai, China; Jiangsu Collaborative Innovation Center of Atmospheric Environment and Equipment Technology (CICAEET), Nanjing University of Information Science & Technology, Nanjing, 210044.
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34
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Stanley CE, Grossmann G, i Solvas XC, deMello AJ. Soil-on-a-Chip: microfluidic platforms for environmental organismal studies. LAB ON A CHIP 2016; 16:228-41. [PMID: 26645910 DOI: 10.1039/c5lc01285f] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Soil is the habitat of countless organisms and encompasses an enormous variety of dynamic environmental conditions. While it is evident that a thorough understanding of how organisms interact with the soil environment may have substantial ecological and economical impact, current laboratory-based methods depend on reductionist approaches that are incapable of simulating natural diversity. The application of Lab-on-a-Chip or microfluidic technologies to organismal studies is an emerging field, where the unique benefits afforded by system miniaturisation offer new opportunities for the experimentalist. Indeed, precise spatiotemporal control over the microenvironments of soil organisms in combination with high-resolution imaging has the potential to provide an unprecedented view of biological events at the single-organism or single-cell level, which in turn opens up new avenues for environmental and organismal studies. Herein we review some of the most recent and interesting developments in microfluidic technologies for the study of soil organisms and their interactions with the environment. We discuss how so-called "Soil-on-a-Chip" technology has already contributed significantly to the study of bacteria, nematodes, fungi and plants, as well as inter-organismal interactions, by advancing experimental access and environmental control. Most crucially, we highlight where distinct advantages over traditional approaches exist and where novel biological insights will ensue.
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Affiliation(s)
- Claire E Stanley
- Institute of Chemical and Bioengineering, ETH Zürich, Vladimir-Prelog-Weg 1, 8093 Zürich, Switzerland.
| | - Guido Grossmann
- Cell Networks-Cluster of Excellence and Centre for Organismal Studies (COS) Heidelberg, Universität Heidelberg, 69120 Heidelberg, Germany
| | | | - Andrew J deMello
- Institute of Chemical and Bioengineering, ETH Zürich, Vladimir-Prelog-Weg 1, 8093 Zürich, Switzerland.
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35
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Lind KR, Sizmur T, Benomar S, Miller A, Cademartiri L. LEGO® bricks as building blocks for centimeter-scale biological environments: the case of plants. PLoS One 2014; 9:e100867. [PMID: 24963716 PMCID: PMC4071033 DOI: 10.1371/journal.pone.0100867] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 05/31/2014] [Indexed: 01/21/2023] Open
Abstract
LEGO bricks are commercially available interlocking pieces of plastic that are conventionally used as toys. We describe their use to build engineered environments for cm-scale biological systems, in particular plant roots. Specifically, we take advantage of the unique modularity of these building blocks to create inexpensive, transparent, reconfigurable, and highly scalable environments for plant growth in which structural obstacles and chemical gradients can be precisely engineered to mimic soil.
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Affiliation(s)
- Kara R. Lind
- Department of Materials Science & Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Tom Sizmur
- Department of Materials Science & Engineering, Iowa State University, Ames, Iowa, United States of America
- Ames Laboratory, US Department of Energy, Iowa State University, Ames, Iowa, United States of America
| | - Saida Benomar
- Department of Materials Science & Engineering, Iowa State University, Ames, Iowa, United States of America
- Ames Laboratory, US Department of Energy, Iowa State University, Ames, Iowa, United States of America
| | - Anthony Miller
- Department of Materials Science & Engineering, Iowa State University, Ames, Iowa, United States of America
- Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
| | - Ludovico Cademartiri
- Department of Materials Science & Engineering, Iowa State University, Ames, Iowa, United States of America
- Ames Laboratory, US Department of Energy, Iowa State University, Ames, Iowa, United States of America
- Department of Chemical & Biological Engineering, Iowa State University, Ames, Iowa, United States of America
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36
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Jiang H, Xu Z, Aluru MR, Dong L. Plant chip for high-throughput phenotyping of Arabidopsis. LAB ON A CHIP 2014; 14:1281-93. [PMID: 24510109 DOI: 10.1039/c3lc51326b] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
We report on the development of a vertical and transparent microfluidic chip for high-throughput phenotyping of Arabidopsis thaliana plants. Multiple Arabidopsis seeds can be germinated and grown hydroponically over more than two weeks in the chip, thus enabling large-scale and quantitative monitoring of plant phenotypes. The novel vertical arrangement of this microfluidic device not only allows for normal gravitropic growth of the plants but also, more importantly, makes it convenient to continuously monitor phenotypic changes in plants at the whole organismal level, including seed germination and root and shoot growth (hypocotyls, cotyledons, and leaves), as well as at the cellular level. We also developed a hydrodynamic trapping method to automatically place single seeds into seed holding sites of the device and to avoid potential damage to seeds that might occur during manual loading. We demonstrated general utility of this microfluidic device by showing clear visible phenotypes of the immutans mutant of Arabidopsis, and we also showed changes occurring during plant-pathogen interactions at different developmental stages. Arabidopsis plants grown in the device maintained normal morphological and physiological behaviour, and distinct phenotypic variations consistent with a priori data were observed via high-resolution images taken in real time. Moreover, the timeline for different developmental stages for plants grown in this device was highly comparable to growth using a conventional agar plate method. This prototype plant chip technology is expected to lead to the establishment of a powerful experimental and cost-effective framework for high-throughput and precise plant phenotyping.
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Affiliation(s)
- Huawei Jiang
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA.
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37
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Yang J, Chen Z, Ching P, Shi Q, Li X. An integrated microfluidic platform for evaluating in vivo antimicrobial activity of natural compounds using a whole-animal infection model. LAB ON A CHIP 2013; 13:3373-82. [PMID: 23824379 DOI: 10.1039/c3lc50264c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The nematode Caenorhabditis elegans is a useful model host for pathogenesis research that can be infected by a large number of human pathogens. Conventionally, nematode-pathogen infection assays are mainly performed on agar medium which are labor-intensive and time-consuming. To overcome these challenges, we develop for the first time an integrated microfluidic device for evaluating in vivo antimicrobial activity of natural compounds, which allows infection and anti-infection assays to be sequentially and automatically carried out in liquid medium. The device consists of a worm dispenser with 32 trap-construction chambers and concentration gradient generators, in which the processes of introduction, dispensation, confinement of worms in the chamber and drug delivery to the chamber can be integrated into a single device. In addition, the operation of the device is simple and does not require any expensive robotic fluid handling systems to dispense samples. To demonstrate the ability of this device, we devise an on-line screening experiment using a Caenorhabditis elegans-Staphylococcus aureus infection model and characterize the survival rate of the infected worms treated with antibiotics. Then, we applied the system to evaluate the antibacterial activity of several components of rhubarb: aloe-emodin, rhein and emodin at various concentrations. The device is able to load uniform worms into each chamber within 10 min and then generate various chemical concentrations automatically and simultaneously. Furthermore, the on-chip method only requires 6 h to establish the infection model and 48 h to perform the subsequent treatments. Based on the excellent advantages and scalable properties of microfluidics, the microfluidic platform holds a great potential in high-throughput screening for antimicrobials.
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Affiliation(s)
- Jianping Yang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, PR China
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38
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Sivagnanam V, Gijs MAM. Exploring Living Multicellular Organisms, Organs, and Tissues Using Microfluidic Systems. Chem Rev 2013; 113:3214-47. [DOI: 10.1021/cr200432q] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
| | - Martin A. M. Gijs
- Laboratory
of Microsystems, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne,
Switzerland
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39
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A microfluidic device and computational platform for high-throughput live imaging of gene expression. Nat Methods 2012; 9:1101-6. [PMID: 23023597 PMCID: PMC3492502 DOI: 10.1038/nmeth.2185] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 09/04/2012] [Indexed: 11/08/2022]
Abstract
To fully describe gene expression dynamics requires the ability to quantitatively capture expression in individual cells over time. Automated systems for acquiring and analyzing real-time images are needed to obtain unbiased data across many samples and conditions. We developed a microfluidics device, the RootArray, in which 64 Arabidopsis thaliana seedlings can be grown and their roots imaged by confocal microscopy over several days without manual intervention. To achieve high throughput, we decoupled acquisition from analysis. In the acquisition phase, we obtain images at low resolution and segment to identify regions of interest. Coordinates are communicated to the microscope to record the regions of interest at high resolution. In the analysis phase, we reconstruct three-dimensional objects from stitched high-resolution images and extract quantitative measurements from a virtual medial section of the root. We tracked hundreds of roots to capture detailed expression patterns of 12 transgenic reporter lines under different conditions.
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