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You HJ, Jo H, Kim JM, Kang ST, Luong NH, Kim YH, Lee S. Exploration and genetic analyses of canopy leaf pigmentation changes in soybean (Glycine max L.): unveiling a novel phenotype. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:202. [PMID: 39134894 PMCID: PMC11319514 DOI: 10.1007/s00122-024-04693-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 07/04/2024] [Indexed: 08/15/2024]
Abstract
KEY MESSAGE Pigmentation changes in canopy leaves were first reported, and subsequent genetic analyses identified a major QTL associated with levels of pigmentation changes, suggesting Glyma.06G202300 as a candidate gene. An unexpected reddish-purple pigmentation in upper canopy leaves was discovered during the late reproductive stages in soybean (Glycine max L.) genotypes. Two sensitive genotypes, 'Uram' and PI 96983, exhibited anomalous canopy leaf pigmentation changes (CLPC), while 'Daepung' did not. The objectives of this study were to: (i) characterize the physiological features of pigmented canopy leaves compared with non-pigmented leaves, (ii) evaluate phenotypic variation in a combined recombinant inbred line (RIL) population (N = 169 RILs) under field conditions, and (iii) genetically identify quantitative trait loci (QTL) for CLPC via joint population linkage analysis. Comparison between pigmented and normal leaves revealed different Fv/Fm of photosystem II, hyperspectral reflectance, and cellular properties, suggesting the pigmentation changes occur in response to an undefined abiotic stress. A highly significant QTL was identified on chromosome 6, explaining ~ 62.8% of phenotypic variance. Based on the QTL result, Glyma.06G202300 encoding flavonoid 3'-hydroxylase (F3'H) was identified as a candidate gene. In both Uram and PI 96983, a 1-bp deletion was confirmed in the third exon of Glyma.06G202300 that results in a premature stop codon in both Uram and PI 96983 and a truncated F3'H protein lacking important domains. Additionally, gene expression analyses uncovered significant differences between pigmented and non-pigmented leaves. This is the first report of a novel symptom and an associated major QTL. These results will provide soybean geneticists and breeders with valuable knowledge regarding physiological changes that may affect soybean production. Further studies are required to elucidate the causal environmental stress and the underlying molecular mechanisms.
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Affiliation(s)
- Hee Jin You
- Department of Crop Science, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 34134, South Korea
| | - Hyun Jo
- Department of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, South Korea
| | - Ji-Min Kim
- Department of Crop Science and Biotechnology, College of Bioresource Science, Dankook University, Cheonan, Chungnam, 31116, South Korea
| | - Sung-Taeg Kang
- Department of Crop Science and Biotechnology, College of Bioresource Science, Dankook University, Cheonan, Chungnam, 31116, South Korea
| | - Ngoc Ha Luong
- Department of Crop Science, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 34134, South Korea
| | - Yeong-Ho Kim
- Department of Crop Science, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 34134, South Korea
| | - Sungwoo Lee
- Department of Crop Science, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 34134, South Korea.
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2
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Ballentine WM, Dorgan KM. The Meioflume: A New System for Observing the Interstitial Behavior of Meiofauna. Integr Org Biol 2024; 6:obae016. [PMID: 38883566 PMCID: PMC11177882 DOI: 10.1093/iob/obae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 04/27/2024] [Accepted: 05/24/2024] [Indexed: 06/18/2024] Open
Abstract
Meiofauna (benthic invertebrates < 1 mm in size) facilitate sediment biogeochemical cycling, alter sediment microbial community structure, and serve as an important trophic link between benthic micro- and macrofauna, yet the behaviors that mechanistically link individuals to their ecological effects are largely unknown. Meiofauna are small and sediments are opaque, making observing the in situ activities of these animals challenging. We developed the Meioflume, a small, acrylic flow tunnel filled with grains of cryolite, a transparent sand analog, to simulate the in situ conditions experienced by meiofauna in an observable lab environment. The Meioflume has a working area (28.57 mm × 10.16 mm × 1 mm) that is small enough to quickly locate fauna and clearly observe behavior but large enough that animals are not tightly confined. When connected to a syringe press, the Meioflume can produce low velocity flows consistently and evenly across the width of its working area while retaining the contents. To demonstrate its functionality in observing the behavior of meiofauna, we placed individual meiofaunal animals (a protodrilid annelid, a harpacticoid copepod, and a platyhelminth flatworm) in Meioflumes and filmed their behavioral response to a sudden initiation of porewater flow. All animals were clearly visible within the flume and could be observed responding to the onset of flow. The design and construction of the Meioflume make it an accessible, affordable tool for researchers. This experimental system could be modified to address many questions in meiofaunal ecology, such as studying behavior in response to chemical cues, allowing us to observe meiofaunal behaviors to better understand their ecological effects.
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Affiliation(s)
- W M Ballentine
- School of Marine and Environmental Sciences, University of South Alabama, Mobile, AL 36688, USA
- Dauphin Island Sea Lab, Dauphin Island, AL 36528, USA
| | - K M Dorgan
- School of Marine and Environmental Sciences, University of South Alabama, Mobile, AL 36688, USA
- Dauphin Island Sea Lab, Dauphin Island, AL 36528, USA
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3
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Perry RN. Detection of the Effects of Root Exudates (Diffusates) on Nematode Hatching and Attraction. Methods Mol Biol 2024; 2756:271-289. [PMID: 38427299 DOI: 10.1007/978-1-0716-3638-1_8] [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: 03/02/2024]
Abstract
Plant-parasitic nematodes have enormous economic and social impacts. The majority of plant-parasitic nematodes are soil dwelling and feed on plant roots. Exudates from actively growing roots initiate hatch of some nematode species, thus ensuring infective juveniles emerge in close proximity to host plant roots. Several gradients of volatile and non-volatile compounds are established around plant roots, at least some of which are used by nematodes to orientate toward the roots. Plant-parasitic nematodes are microscopic in size (less than 1 mm in length and between 15 and 20 μm in diameter), so investigations into behavior are challenging. Various in vitro techniques have been used to evaluate the effects of root exudates. The techniques can also be used to evaluate the comparative attractiveness of different plants or cultivars of the same plant species. This chapter describes some examples of different types of basic in vitro assays.
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Affiliation(s)
- Roland N Perry
- Department of Biological and Environmental Sciences, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, Hertfordshire, UK.
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4
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Rooney LM, Dupuy LX, Hoskisson PA, McConnell G. Construction and characterisation of a structured, tuneable, and transparent 3D culture platform for soil bacteria. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001429. [PMID: 38289644 PMCID: PMC10866023 DOI: 10.1099/mic.0.001429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/19/2024] [Indexed: 02/01/2024]
Abstract
We have developed a tuneable workflow for the study of soil microbes in an imitative 3D soil environment that is compatible with routine and advanced optical imaging, is chemically customisable, and is reliably refractive index matched based on the carbon catabolism of the study organism. We demonstrate our transparent soil pipeline with two representative soil organisms, Bacillus subtilis and Streptomyces coelicolor, and visualise their colonisation behaviours using fluorescence microscopy and mesoscopy. This spatially structured, 3D approach to microbial culture has the potential to further study the behaviour of bacteria in conditions matching their native environment and could be expanded to study microbial interactions, such as competition and warfare.
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Affiliation(s)
- Liam M. Rooney
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Lionel X. Dupuy
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- Present address: Department of Conservation of Natural Resources, Neiker, Basque Institute for Agricultural Research and Development, Derio, Spain
- Present address: Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Paul A. Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Gail McConnell
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
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5
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Ebrahimi S, Moreno-Pescador G, Persson S, Jauffred L, Bendix PM. Label-free optical interferometric microscopy to characterize morphodynamics in living plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1156478. [PMID: 37284726 PMCID: PMC10239806 DOI: 10.3389/fpls.2023.1156478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/04/2023] [Indexed: 06/08/2023]
Abstract
During the last century, fluorescence microscopy has played a pivotal role in a range of scientific discoveries. The success of fluorescence microscopy has prevailed despite several shortcomings like measurement time, photobleaching, temporal resolution, and specific sample preparation. To bypass these obstacles, label-free interferometric methods have been developed. Interferometry exploits the full wavefront information of laser light after interaction with biological material to yield interference patterns that contain information about structure and activity. Here, we review recent studies in interferometric imaging of plant cells and tissues, using techniques such as biospeckle imaging, optical coherence tomography, and digital holography. These methods enable quantification of cell morphology and dynamic intracellular measurements over extended periods of time. Recent investigations have showcased the potential of interferometric techniques for precise identification of seed viability and germination, plant diseases, plant growth and cell texture, intracellular activity and cytoplasmic transport. We envision that further developments of these label-free approaches, will allow for high-resolution, dynamic imaging of plants and their organelles, ranging in scales from sub-cellular to tissue and from milliseconds to hours.
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Affiliation(s)
- Samira Ebrahimi
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- Biocomplexity, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Guillermo Moreno-Pescador
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- Biocomplexity, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Staffan Persson
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Liselotte Jauffred
- Biocomplexity, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Poul Martin Bendix
- Biocomplexity, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
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6
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Light Microscopy Technologies and the Plant Cytoskeleton. Methods Mol Biol 2023; 2604:337-352. [PMID: 36773248 DOI: 10.1007/978-1-0716-2867-6_28] [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: 02/12/2023]
Abstract
The cytoskeleton is a dynamic and diverse subcellular filament network, and as such microscopy is an essential technology to enable researchers to study and characterize these systems. Microscopy has a long history of observing the plant world not least as the subject where Robert Hooke coined the term "cell" in his publication Micrographia. From early observations of plant morphology to today's advanced super-resolution technologies, light microscopy is the indispensable tool for the plant cell biologist. In this mini review, we will discuss some of the major modalities used to examine the plant cytoskeleton and the theory behind them.
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7
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Paré L, Banchini C, Hamel C, Bernier L, Stefani F. A simple and low-cost technique to initiate single-spore cultures of arbuscular mycorrhizal fungi using a superabsorbent polymer. Symbiosis 2022. [DOI: 10.1007/s13199-022-00878-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
AbstractMost species of arbuscular mycorrhizal fungi (AMF) are propagated with a host plant in a pot culture. However, the soil matrix makes it difficult to monitor the establishment and development of the symbiosis. In vitro culturing using Ri T-DNA transformed roots provides a clear medium and a sterile environment which offsets the constraints of the soil matrix. Nevertheless, the sterile conditions and the Ri T-DNA transformed roots provide very different growing conditions compared to a pot culture. Transparent soil based on superabsorbent polymer (SAP) has the potential of combining the advantages of current in vivo and in vitro culture methods without the constraints associated with either technique (opacity and sterility). Here we describe a SAP-based autotrophic culture as an alternative to current in vivo and in vitro culture methods. This system using two-compartment Petri dishes makes it easy to initiate single-spore cultures and to monitor fungal propagation. The SAP-based autotrophic system allowed the establishment of single-spore cultures of seven species (Diversispora varaderana, Funneliformis geosporus, Gigaspora rosea, Racocetra fulgida, Rhizophagus irregularis, R. intraradices and Sclerocystis sp.) from six genera and three families. Cultures were maintained over several months under non-sterile conditions. The Petri dishes avoid the problem of cross contamination and they can be stacked for space optimization. The grains of SAP colonized with new spores were used as inoculum to initiate new cultures in the SAP-based system. The SAP-based autotrophic culture method is a low-cost and low-tech approach, which makes the study of AMF much more accessible.
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Engelhardt IC, Patko D, Liu Y, Mimault M, de Las Heras Martinez G, George TS, MacDonald M, Ptashnyk M, Sukhodub T, Stanley-Wall NR, Holden N, Daniell TJ, Dupuy LX. Novel form of collective movement by soil bacteria. THE ISME JOURNAL 2022; 16:2337-2347. [PMID: 35798939 PMCID: PMC9478162 DOI: 10.1038/s41396-022-01277-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 06/07/2022] [Accepted: 06/17/2022] [Indexed: 04/16/2023]
Abstract
Although migrations are essential for soil microorganisms to exploit scarce and heterogeneously distributed resources, bacterial mobility in soil remains poorly studied due to experimental limitations. In this study, time-lapse images collected using live microscopy techniques captured collective and coordinated groups of B. subtilis cells exhibiting "crowd movement". Groups of B. subtilis cells moved through transparent soil (nafion polymer with particle size resembling sand) toward plant roots and re-arranged dynamically around root tips in the form of elongating and retracting "flocks" resembling collective behaviour usually associated with higher organisms (e.g., bird flocks or fish schools). Genetic analysis reveals B. subtilis flocks are likely driven by the diffusion of extracellular signalling molecules (e.g., chemotaxis, quorum sensing) and may be impacted by the physical obstacles and hydrodynamics encountered in the soil like environment. Our findings advance understanding of bacterial migration through soil matrices and expand known behaviours for coordinated bacterial movement.
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Affiliation(s)
- I C Engelhardt
- Ecological Sciences, The James Hutton Institute, Dundee, UK
- Department of Conservation of Natural Resources, Neiker, Bilbao, Spain
| | - D Patko
- Ecological Sciences, The James Hutton Institute, Dundee, UK
- Department of Conservation of Natural Resources, Neiker, Bilbao, Spain
| | - Y Liu
- Ecological Sciences, The James Hutton Institute, Dundee, UK
- ICS, The James Hutton Institute, Dundee, UK
| | - M Mimault
- ICS, The James Hutton Institute, Dundee, UK
| | | | - T S George
- Ecological Sciences, The James Hutton Institute, Dundee, UK
| | - M MacDonald
- School of Science and Engineering, University of Dundee, Dundee, UK
| | - M Ptashnyk
- School of Mathematical & Computer Sciences, Heriot-Watt University, Edinburgh, UK
| | - T Sukhodub
- School of Life Sciences, University of Dundee, Dundee, UK
| | | | - N Holden
- Ecological Sciences, The James Hutton Institute, Dundee, UK
- North Faculty, Scotland's Rural College, Aberdeen, UK
| | - T J Daniell
- Plants, Photosynthesis and Soil, School of Biosciences, The University of Sheffield, Sheffield, UK
| | - L X Dupuy
- Ecological Sciences, The James Hutton Institute, Dundee, UK.
- Department of Conservation of Natural Resources, Neiker, Bilbao, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
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9
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Ovečka M, Sojka J, Tichá M, Komis G, Basheer J, Marchetti C, Šamajová O, Kuběnová L, Šamaj J. Imaging plant cells and organs with light-sheet and super-resolution microscopy. PLANT PHYSIOLOGY 2022; 188:683-702. [PMID: 35235660 PMCID: PMC8825356 DOI: 10.1093/plphys/kiab349] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/12/2021] [Indexed: 05/05/2023]
Abstract
The documentation of plant growth and development requires integrative and scalable approaches to investigate and spatiotemporally resolve various dynamic processes at different levels of plant body organization. The present update deals with vigorous developments in mesoscopy, microscopy and nanoscopy methods that have been translated to imaging of plant subcellular compartments, cells, tissues and organs over the past 3 years with the aim to report recent applications and reasonable expectations from current light-sheet fluorescence microscopy (LSFM) and super-resolution microscopy (SRM) modalities. Moreover, the shortcomings and limitations of existing LSFM and SRM are discussed, particularly for their ability to accommodate plant samples and regarding their documentation potential considering spherical aberrations or temporal restrictions prohibiting the dynamic recording of fast cellular processes at the three dimensions. For a more comprehensive description, advances in living or fixed sample preparation methods are also included, supported by an overview of developments in labeling strategies successfully applied in plants. These strategies are practically documented by current applications employing model plant Arabidopsis thaliana (L.) Heynh., but also robust crop species such as Medicago sativa L. and Hordeum vulgare L. Over the past few years, the trend towards designing of integrative microscopic modalities has become apparent and it is expected that in the near future LSFM and SRM will be bridged to achieve broader multiscale plant imaging with a single platform.
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Affiliation(s)
- Miroslav Ovečka
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Jiří Sojka
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Michaela Tichá
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - George Komis
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Jasim Basheer
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Cintia Marchetti
- Centre of the Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Olga Šamajová
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Lenka Kuběnová
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Jozef Šamaj
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
- Author for communication:
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Liu Y, Patko D, Engelhardt I, George TS, Stanley-Wall NR, Ladmiral V, Ameduri B, Daniell TJ, Holden N, MacDonald MP, Dupuy LX. Plant-environment microscopy tracks interactions of Bacillus subtilis with plant roots across the entire rhizosphere. Proc Natl Acad Sci U S A 2021; 118:e2109176118. [PMID: 34819371 PMCID: PMC8640753 DOI: 10.1073/pnas.2109176118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2021] [Indexed: 11/18/2022] Open
Abstract
Our understanding of plant-microbe interactions in soil is limited by the difficulty of observing processes at the microscopic scale throughout plants' large volume of influence. Here, we present the development of three-dimensional live microscopy for resolving plant-microbe interactions across the environment of an entire seedling growing in a transparent soil in tailor-made mesocosms, maintaining physical conditions for the culture of both plants and microorganisms. A tailor-made, dual-illumination light sheet system acquired photons scattered from the plant while fluorescence emissions were simultaneously captured from transparent soil particles and labeled microorganisms, allowing the generation of quantitative data on samples ∼3,600 mm3 in size, with as good as 5 µm resolution at a rate of up to one scan every 30 min. The system tracked the movement of Bacillus subtilis populations in the rhizosphere of lettuce plants in real time, revealing previously unseen patterns of activity. Motile bacteria favored small pore spaces over the surface of soil particles, colonizing the root in a pulsatile manner. Migrations appeared to be directed toward the root cap, the point of "first contact," before the subsequent colonization of mature epidermis cells. Our findings show that microscopes dedicated to live environmental studies present an invaluable tool to understand plant-microbe interactions.
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Affiliation(s)
- Yangminghao Liu
- School of Science and Engineering, University of Dundee, Dundee DD1 4HN, United Kingdom
| | - Daniel Patko
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
- Department of Conservation of Natural Resources, Neiker, Derio 48160, Spain
| | - Ilonka Engelhardt
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
- Department of Conservation of Natural Resources, Neiker, Derio 48160, Spain
| | - Timothy S George
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | | | - Vincent Ladmiral
- Institut Charles Gerhardt de Montpellier, Université de Montpellier, CNRS, ENSCM, Montpellier 34090, France
| | - Bruno Ameduri
- Institut Charles Gerhardt de Montpellier, Université de Montpellier, CNRS, ENSCM, Montpellier 34090, France
| | - Tim J Daniell
- Plants, Photosynthesis and Soil, School of Biosciences, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Nicola Holden
- Northern Faculty, Scotland's Rural College, Aberdeen AB21 9YA, United Kingdom
| | - Michael P MacDonald
- School of Science and Engineering, University of Dundee, Dundee DD1 4HN, United Kingdom;
| | - Lionel X Dupuy
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom;
- Department of Conservation of Natural Resources, Neiker, Derio 48160, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao 48009, Spain
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11
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Methods for Studying Bacterial–Fungal Interactions in the Microenvironments of Soil. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11199182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Due to their small size, microorganisms directly experience only a tiny portion of the environmental heterogeneity manifested in the soil. The microscale variations in soil properties constrain the distribution of fungi and bacteria, and the extent to which they can interact with each other, thereby directly influencing their behavior and ecological roles. Thus, to obtain a realistic understanding of bacterial–fungal interactions, the spatiotemporal complexity of their microenvironments must be accounted for. The objective of this review is to further raise awareness of this important aspect and to discuss an overview of possible methodologies, some of easier applicability than others, that can be implemented in the experimental design in this field of research. The experimental design can be rationalized in three different scales, namely reconstructing the physicochemical complexity of the soil matrix, identifying and locating fungi and bacteria to depict their physical interactions, and, lastly, analyzing their molecular environment to describe their activity. In the long term, only relevant experimental data at the cell-to-cell level can provide the base for any solid theory or model that may serve for accurate functional prediction at the ecosystem level. The way to this level of application is still long, but we should all start small.
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Ge S, Dupuy LX, MacDonald MP. In situ laser manipulation of root tissues in transparent soil. PLANT AND SOIL 2021; 468:475-489. [PMID: 34789948 PMCID: PMC8580905 DOI: 10.1007/s11104-021-05133-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
AIMS Laser micromanipulation such as dissection or optical trapping enables remote physical modification of the activity of tissues, cells and organelles. To date, applications of laser manipulation to plant roots grown in soil have been limited. Here, we show laser manipulation can be applied in situ when plant roots are grown in transparent soil. METHODS We have developed a Q-switched laser manipulation and imaging instrument to perform controlled dissection of roots and to study light-induced root growth responses. We performed a detailed characterisation of the properties of the cutting beams through the soil, studying dissection and optical ablation. Furthermore, we also studied the use of low light doses to control the root elongation rate of lettuce seedlings (Lactuca sativa) in air, agar, gel and transparent soil. RESULTS We show that whilst soil inhomogeneities affect the thickness and circularity of the beam, those distortions are not inherently limiting. The ability to induce changes in root elongation or complete dissection of microscopic regions of the root is robust to substrate heterogeneity and microscopy set up and is maintained following the limited distortions induced by the transparent soil environment. CONCLUSIONS Our findings show that controlled in situ laser dissection of root tissues is possible with a simple and low-cost optical set-up. We also show that, in the absence of dissection, a reduced laser light power density can provide reversible control of root growth, achieving a precise "point and shoot" method for root manipulation.
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Affiliation(s)
- Sisi Ge
- School of Science and Engineering, University of Dundee, Nethergate, Dundee, DD1 4HN UK
| | - Lionel X. Dupuy
- Neiker, Department of Conservation of Natural Resources, Berreaga 1, 48.160, Derio, Spain
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
- IKERBASQUE, Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Spain
| | - Michael P. MacDonald
- School of Science and Engineering, University of Dundee, Nethergate, Dundee, DD1 4HN UK
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13
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Eves-van den Akker S. Plant-nematode interactions. CURRENT OPINION IN PLANT BIOLOGY 2021; 62:102035. [PMID: 33784578 DOI: 10.1016/j.pbi.2021.102035] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 02/05/2021] [Accepted: 02/23/2021] [Indexed: 05/27/2023]
Abstract
Plant-parasitic nematodes threaten food security in the developed and developing world. This review looks at the field through a wide lens, aiming to capture a breadth of recent landmark achievements that have changed our understanding of plant-nematode interactions in particular, and plant pathology in general. It recognises the importance of expanding existing paradigms in plant-pathology to encompass plant-nematode interactions and, at the same time, celebrates achievements that build on the uniqueness of the system. It highlights emerging areas of plant nematology. Finally, it argues that the accelerated progress of recent years is prophetic, and that cumulative advances in our understanding, coupled with technological advances in genetic engineering of plants and nematodes, promise to lift perennial constraints on the field and thereby further expedite progress.
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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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Sharma K, Palatinszky M, Nikolov G, Berry D, Shank EA. Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms. eLife 2020; 9:e56275. [PMID: 33140722 PMCID: PMC7609051 DOI: 10.7554/elife.56275] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 10/16/2020] [Indexed: 01/02/2023] Open
Abstract
Microscale processes are critically important to soil ecology and biogeochemistry yet are difficult to study due to soil's opacity and complexity. To advance the study of soil processes, we constructed transparent soil microcosms that enable the visualization of microbes via fluorescence microscopy and the non-destructive measurement of microbial activity and carbon uptake in situ via Raman microspectroscopy. We assessed the polymer Nafion and the crystal cryolite as optically transparent soil substrates. We demonstrated that both substrates enable the growth, maintenance, and visualization of microbial cells in three dimensions over time, and are compatible with stable isotope probing using Raman. We applied this system to ascertain that after a dry-down/rewetting cycle, bacteria on and near dead fungal hyphae were more metabolically active than those far from hyphae. These data underscore the impact fungi have facilitating bacterial survival in fluctuating conditions and how these microcosms can yield insights into microscale microbial activities.
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Affiliation(s)
- Kriti Sharma
- Department of Biology, University of North CarolinaChapel HillUnited States
| | - Márton Palatinszky
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of ViennaViennaAustria
| | - Georgi Nikolov
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of ViennaViennaAustria
| | - David Berry
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of ViennaViennaAustria
| | - Elizabeth A Shank
- Department of Biology, University of North CarolinaChapel HillUnited States
- Department of Microbiology and Immunology, University of North CarolinaChapel HillUnited States
- Program in Systems Biology, University of Massachusetts Medical SchoolWorcesterUnited States
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Harvey HJ, Wildman RD, Mooney SJ, Avery SV. Challenges and approaches in assessing the interplay between microorganisms and their physical micro-environments. Comput Struct Biotechnol J 2020; 18:2860-2866. [PMID: 33133427 PMCID: PMC7588748 DOI: 10.1016/j.csbj.2020.09.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/22/2022] Open
Abstract
Spatial structure over scales ranging from nanometres to centimetres (and beyond) varies markedly in diverse habitats and the industry-relevant settings that support microbial activity. Developing an understanding of the interplay between a structured environment and the associated microbial processes and ecology is fundamental, but challenging. Several novel approaches have recently been developed and implemented to help address key questions for the field: from the use of imaging tools such as X-ray Computed Tomography to explore microbial growth in soils, to the fabrication of scratched materials to examine microbial-surface interactions, to the design of microfluidic devices to track microbial biofilm formation and the metabolic processes therein. This review discusses new approaches and challenges for incorporating structured elements into the study of microbial processes across different scales. We highlight how such methods can be pivotal for furthering our understanding of microbial interactions with their environments.
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Affiliation(s)
- Harry J. Harvey
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Ricky D. Wildman
- Faculty of Engineering, University of Nottingham, Nottingham, UK
| | - Sacha J. Mooney
- School of Biosciences, University of Nottingham, Nottingham, UK
| | - Simon V. Avery
- School of Life Sciences, University of Nottingham, Nottingham, UK
- Corresponding author.
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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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O’Callaghan FE, Neilson R, MacFarlane SA, Dupuy LX. Dynamic biospeckle analysis, a new tool for the fast screening of plant nematicide selectivity. PLANT METHODS 2019; 15:155. [PMID: 31889979 PMCID: PMC6921579 DOI: 10.1186/s13007-019-0523-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/09/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Plant feeding, free-living nematodes cause extensive damage to plant roots by direct feeding and, in the case of some trichodorid and longidorid species, through the transmission of viruses. Developing more environmentally friendly, target-specific nematicides is currently impeded by slow and laborious methods of toxicity testing. Here, we developed a bioactivity assay based on the dynamics of light 'speckle' generated by living cells and we demonstrate its application by assessing chemicals' toxicity to different nematode trophic groups. RESULTS Free-living nematode populations extracted from soil were exposed to methanol and phenyl isothiocyanate (PEITC). Biospeckle analysis revealed differing behavioural responses as a function of nematode feeding groups. Trichodorus nematodes were less sensitive than were bacterial feeding nematodes or non-trichodorid plant feeding nematodes. Following 24 h of exposure to PEITC, bioactivity significantly decreased for plant and bacterial feeders but not for Trichodorus nematodes. Decreases in movement for plant and bacterial feeders in the presence of PEITC also led to measurable changes to the morphology of biospeckle patterns. CONCLUSIONS Biospeckle analysis can be used to accelerate the screening of nematode bioactivity, thereby providing a fast way of testing the specificity of potential nematicidal compounds. With nematodes' distinctive movement and activity levels being visible in the biospeckle pattern, the technique has potential to screen the behavioural responses of diverse trophic nematode communities. The method discriminates both behavioural responses, morphological traits and activity levels and hence could be used to assess the specificity of nematicidal compounds.
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Affiliation(s)
| | - Roy Neilson
- The James Hutton Institute, Invergowrie, Dundee, D2 5DA Scotland, UK
| | | | - Lionel X. Dupuy
- The James Hutton Institute, Invergowrie, Dundee, D2 5DA Scotland, UK
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19
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Ovečka M, von Wangenheim D, Tomančák P, Šamajová O, Komis G, Šamaj J. Multiscale imaging of plant development by light-sheet fluorescence microscopy. NATURE PLANTS 2018; 4:639-650. [PMID: 30185982 DOI: 10.1038/s41477-018-0238-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/31/2018] [Indexed: 05/21/2023]
Abstract
Light-sheet fluorescence microscopy (LSFM) methods collectively represent the major breakthrough in developmental bio-imaging of living multicellular organisms. They are becoming a mainstream approach through the development of both commercial and custom-made LSFM platforms that are adjusted to diverse biological applications. Based on high-speed acquisition rates under conditions of low light exposure and minimal photo-damage of the biological sample, these methods provide ideal means for long-term and in-depth data acquisition during organ imaging at single-cell resolution. The introduction of LSFM methods into biology extended our understanding of pattern formation and developmental progress of multicellular organisms from embryogenesis to adult body. Moreover, LSFM imaging allowed the dynamic visualization of biological processes under almost natural conditions. Here, we review the most important, recent biological applications of LSFM methods in developmental studies of established and emerging plant model species, together with up-to-date methods of data editing and evaluation for modelling of complex biological processes. Recent applications in animal models push LSFM into the forefront of current bio-imaging approaches. Since LSFM is now the single most effective method for fast imaging of multicellular organisms, allowing quantitative analyses of their long-term development, its broader use in plant developmental biology will likely bring new insights.
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Affiliation(s)
- Miroslav Ovečka
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czech Republic
| | - Daniel von Wangenheim
- Plant Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Pavel Tomančák
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Olga Šamajová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czech Republic
| | - George Komis
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czech Republic
| | - Jozef Šamaj
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czech Republic.
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20
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Micromechanics of root development in soil. Curr Opin Genet Dev 2018; 51:18-25. [DOI: 10.1016/j.gde.2018.03.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/04/2018] [Accepted: 03/08/2018] [Indexed: 11/17/2022]
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21
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Sergaki C, Lagunas B, Lidbury I, Gifford ML, Schäfer P. Challenges and Approaches in Microbiome Research: From Fundamental to Applied. FRONTIERS IN PLANT SCIENCE 2018; 9:1205. [PMID: 30174681 PMCID: PMC6107787 DOI: 10.3389/fpls.2018.01205] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/26/2018] [Indexed: 05/07/2023]
Abstract
We face major agricultural challenges that remain a threat for global food security. Soil microbes harbor enormous potentials to provide sustainable and economically favorable solutions that could introduce novel approaches to improve agricultural practices and, hence, crop productivity. In this review we give an overview regarding the current state-of-the-art of microbiome research by discussing new technologies and approaches. We also provide insights into fundamental microbiome research that aim to provide a deeper understanding of the dynamics within microbial communities, as well as their interactions with different plant hosts and the environment. We aim to connect all these approaches with potential applications and reflect how we can use microbial communities in modern agricultural systems to realize a more customized and sustainable use of valuable resources (e.g., soil).
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Affiliation(s)
- Chrysi Sergaki
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- *Correspondence: Chrysi Sergaki,
| | - Beatriz Lagunas
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Ian Lidbury
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Miriam L. Gifford
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, United Kingdom
| | - Patrick Schäfer
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, United Kingdom
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