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Fatima A, Kataria S, Jain M, Prajapati R, Mahawar L. Synchrotron tomography of magnetoprimed soybean plant root system architecture grown in arsenic-polluted soil. FRONTIERS IN PLANT SCIENCE 2024; 15:1391846. [PMID: 39015294 PMCID: PMC11249557 DOI: 10.3389/fpls.2024.1391846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/30/2024] [Indexed: 07/18/2024]
Abstract
The present study evaluated the repercussions of magnetopriming on the root system architecture of soybean plants subjected to arsenic toxicity using synchrotron radiation source based micro-computed tomography (SR-µCT). This will be used evey where as abbreviation for the technique for three-dimensional imaging. Seeds of soybean were exposed to the static magnetic field (SMF) of strength (200 mT) for 1h prior to sowing. Magnetoprimed and non-primed seeds were grown for 1 month in a soil-sand mixture containing four different levels of sodium arsenate (0, 5, 10, and 50 mg As kg-1 soil). The results showed that arsenic adversely affects the root growth in non-primed plants by reducing their root length, root biomass, root hair, size and number of root nodules, where the damaging effect of As was observed maximum at higher concentrations (10 and 50 mg As kg-1 soil). However, a significant improvement in root morphology was detected in magnetoprimed plants where SMF pretreatment enhanced the root length, root biomass, pore diameter of cortical cells, root hair formation, lateral roots branching, and size of root nodules and girth of primary roots. Qualitative analysis of x-ray micro-CT images showed that arsenic toxicity damaged the epidermal and cortical layers of the root as well as reduced the pore diameter of the cortical cells. However, the diameter of cortical cells pores in magnetoprimed plants was observed higher as compared to plants emerged from non-primed seeds at all level of As toxicity. Thus, the study suggested that magnetopriming has the potential to attenuate the toxic effect of As and could be employed as a pre-sowing treatment to reduce the phytotoxic effects of metal ions in plants by improving root architecture and root tolerance index. This study is the very first exploration of the potential benefits of magnetopriming in mitigating the toxicity of metals (As) in plant roots utilizing the micro-CT technique.
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Affiliation(s)
- Anis Fatima
- Technical Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Sunita Kataria
- School of Biochemistry, Devi AhilyaVishwavidyalaya, Indore, MP, India
- Department of Plant Physiology, Faculty of Agrobiology and Food Resource, Slovak University of Agriculture, Nitra, Slovakia
| | - Meeta Jain
- School of Biochemistry, Devi AhilyaVishwavidyalaya, Indore, MP, India
| | | | - Lovely Mahawar
- Department of Plant Physiology, Faculty of Agrobiology and Food Resource, Slovak University of Agriculture, Nitra, Slovakia
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
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Ahkami AH, Qafoku O, Roose T, Mou Q, Lu Y, Cardon ZG, Wu Y, Chou C, Fisher JB, Varga T, Handakumbura P, Aufrecht JA, Bhattacharjee A, Moran JJ. Emerging sensing, imaging, and computational technologies to scale nano-to macroscale rhizosphere dynamics - Review and research perspectives. SOIL BIOLOGY & BIOCHEMISTRY 2024; 189:109253. [PMID: 39238778 PMCID: PMC11376622 DOI: 10.1016/j.soilbio.2023.109253] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/07/2024]
Abstract
The soil region influenced by plant roots, i.e., the rhizosphere, is one of the most complex biological habitats on Earth and significantly impacts global carbon flow and transformation. Understanding the structure and function of the rhizosphere is critically important for maintaining sustainable plant ecosystem services, designing engineered ecosystems for long-term soil carbon storage, and mitigating the effects of climate change. However, studying the biological and ecological processes and interactions in the rhizosphere requires advanced integrated technologies capable of decoding such a complex system at different scales. Here, we review how emerging approaches in sensing, imaging, and computational modeling can advance our understanding of the complex rhizosphere system. Particularly, we provide our perspectives and discuss future directions in developing in situ rhizosphere sensing technologies that could potentially correlate local-scale interactions to ecosystem scale impacts. We first review integrated multimodal imaging techniques for tracking inorganic elements and organic carbon flow at nano- to microscale in the rhizosphere, followed by a discussion on the use of synthetic soil and plant habitats that bridge laboratory-to-field studies on the rhizosphere processes. We then describe applications of genetically encoded biosensors in monitoring nutrient and chemical exchanges in the rhizosphere, and the novel nanotechnology-mediated delivery approaches for introducing biosensors into the root tissues. Next, we review the recent progress and express our vision on field-deployable sensing technologies such as planar optodes for quantifying the distribution of chemical and analyte gradients in the rhizosphere under field conditions. Moreover, we provide perspectives on the challenges of linking complex rhizosphere interactions to ecosystem sensing for detecting biological traits across scales, which arguably requires using the best-available model predictions including the model-experiment and image-based modeling approaches. Experimental platforms relevant to field conditions like SMART (Sensors at Mesoscales with Advanced Remote Telemetry) soils testbed, coupled with ecosystem sensing and predictive models, can be effective tools to explore coupled ecosystem behavior and responses to environmental perturbations. Finally, we envision that with the advent of novel high-resolution imaging capabilities at nano- to macroscale, and remote biosensing technologies, combined with advanced computational models, future studies will lead to detection and upscaling of rhizosphere processes toward ecosystem and global predictions.
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Affiliation(s)
- Amir H Ahkami
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, 99454, USA
| | - Odeta Qafoku
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, 99454, USA
| | - Tiina Roose
- Bioengineering Sciences Research Group, Faculty of Engineering and Environment, University of Southampton, University Road, Southampton, England, SO17 1BJ
| | - Quanbing Mou
- Department of Chemistry, The University of Texas at Austin, 105 East 24 Street, Austin, TX 78712, USA
| | - Yi Lu
- Department of Chemistry, The University of Texas at Austin, 105 East 24 Street, Austin, TX 78712, USA
| | - Zoe G Cardon
- Ecosystems Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Yuxin Wu
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 USA
| | - Chunwei Chou
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 USA
| | - Joshua B Fisher
- Schmid College of Science and Technology, Chapman University, 1 University Drive, Orange, CA, 92866, USA
| | - Tamas Varga
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, 99454, USA
| | - Pubudu Handakumbura
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, 99454, USA
| | - Jayde A Aufrecht
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, 99454, USA
| | - Arunima Bhattacharjee
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, 99454, USA
| | - James J Moran
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, 99454, USA
- Michigan State University, Department of Integrative Biology and Department of Plant, Soil, and Microbial Sciences, East Lansing, MI, 48824, USA
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Duddek P, Ahmed MA, Javaux M, Vanderborght J, Lovric G, King A, Carminati A. The effect of root hairs on root water uptake is determined by root-soil contact and root hair shrinkage. THE NEW PHYTOLOGIST 2023; 240:2484-2497. [PMID: 37525254 DOI: 10.1111/nph.19144] [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: 05/24/2023] [Accepted: 06/29/2023] [Indexed: 08/02/2023]
Abstract
The effect of root hairs on water uptake remains controversial. In particular, the key root hair and soil parameters that determine their importance have been elusive. We grew maize plants (Zea mays) in microcosms and scanned them using synchrotron-based X-ray computed microtomography. By means of image-based modelling, we investigated the parameters determining the effectiveness of root hairs in root water uptake. We explicitly accounted for rhizosphere features (e.g. root-soil contact and pore structure) and took root hair shrinkage of dehydrated root hairs into consideration. Our model suggests that > 85% of the variance in root water uptake is explained by the hair-induced increase in root-soil contact. In dry soil conditions, root hair shrinkage reduces the impact of hairs substantially. We conclude that the effectiveness of root hairs on root water uptake is determined by the hair-induced increase in root-soil contact and root hair shrinkage. Although the latter clearly reduces the effect of hairs on water uptake, our model still indicated facilitation of water uptake by root hairs at soil matric potentials from -1 to -0.1 MPa. Our findings provide new avenues towards a mechanistic understanding of the role of root hairs on water uptake.
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Affiliation(s)
- Patrick Duddek
- Department of Environmental Systems Science, Physics of Soils and Terrestrial Ecosystems, Institute of Terrestrial Ecosystems, ETH Zürich, Universitätsstrasse 16, 8092, Zurich, Switzerland
| | - Mutez Ali Ahmed
- Root-Soil Interactions, School of Life Sciences, Technical University of Munich, D-85354, Freising, Germany
| | - Mathieu Javaux
- Agrosphere Institute, IBG-3, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Jan Vanderborght
- Agrosphere Institute, IBG-3, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Goran Lovric
- Swiss Light Source, Paul Scherrer Institute, Forschungsstrasse 111, 5232, Villigen, Switzerland
| | - Andrew King
- Synchrotron SOLEIL, L'Orme des Merisiers, 91192, Gif-sur-Yvette Cedex, France
| | - Andrea Carminati
- Department of Environmental Systems Science, Physics of Soils and Terrestrial Ecosystems, Institute of Terrestrial Ecosystems, ETH Zürich, Universitätsstrasse 16, 8092, Zurich, Switzerland
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Boursiac Y, Bauget F. Do roots need a good haircut for water uptake? THE NEW PHYTOLOGIST 2023; 240:2173-2175. [PMID: 37845816 DOI: 10.1111/nph.19336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
This article is a Commentary on Duddek et al. (2023), 240: 2484–2497.
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Affiliation(s)
- Yann Boursiac
- Institute for Plant Sciences of Montpellier (IPSiM), Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Fabrice Bauget
- Institute for Plant Sciences of Montpellier (IPSiM), Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
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Le Houx J, Ruiz S, McKay Fletcher D, Ahmed S, Roose T. Statistical Effective Diffusivity Estimation in Porous Media Using an Integrated On-site Imaging Workflow for Synchrotron Users. Transp Porous Media 2023; 150:71-88. [PMID: 37663951 PMCID: PMC10468943 DOI: 10.1007/s11242-023-01993-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 07/03/2023] [Indexed: 09/05/2023]
Abstract
Transport in porous media plays an essential role for many physical, engineering, biological and environmental processes. Novel synchrotron imaging techniques and image-based models have enabled more robust quantification of geometric structures that influence transport through the pore space. However, image-based modelling is computationally expensive, and end users often require, while conducting imaging campaign, fast and agile bulk-scale effective parameter estimates that account for the pore-scale details. In this manuscript we enhance a pre-existing image-based model solver known as OpenImpala to estimate bulk-scale effective transport parameters. In particular, the boundary conditions and equations in OpenImpala were modified in order to estimate the effective diffusivity in an imaged system/geometry via a formal multi-scale homogenisation expansion. Estimates of effective pore space diffusivity were generated for a range of elementary volume sizes to estimate when the effective diffusivity values begin to converge to a single value. Results from OpenImpala were validated against a commercial finite element method package COMSOL Multiphysics (abbreviated as COMSOL). Results showed that the effective diffusivity values determined with OpenImpala were similar to those estimated by COMSOL. Tests on larger domains comparing a full image-based model to a homogenised (geometrically uniform) domain that used the effective diffusivity parameters showed differences below 2 % error, thus verifying the accuracy of the effective diffusivity estimates. Finally, we compared OpenImpala's parallel computing speeds to COMSOL. OpenImpala consistently ran simulations within fractions of minutes, which was two orders of magnitude faster than COMSOL providing identical supercomputing specifications. In conclusion, we demonstrated OpenImpala's utility as part of an on-site tomography processing pipeline allowing for fast and agile assessment of porous media processes and to guide imaging campaigns while they are happening at synchrotron beamlines. Supplementary Information The online version contains supplementary material available at 10.1007/s11242-023-01993-7.
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Affiliation(s)
- James Le Houx
- Department, Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot, Oxfordshire OX11 0DE UK
| | - Siul Ruiz
- Faculty of Engineering and Physical Sciences, University of Southampton, University Road, Southampton, Hampshire SO17 1BJ UK
| | - Daniel McKay Fletcher
- Faculty of Engineering and Physical Sciences, University of Southampton, University Road, Southampton, Hampshire SO17 1BJ UK
- Rural Economy, Environment and Society, Scotland’s Rural College, West Mains Road, Edinburgh, EH9 3JG UK
| | - Sharif Ahmed
- Department, Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot, Oxfordshire OX11 0DE UK
| | - Tiina Roose
- Faculty of Engineering and Physical Sciences, University of Southampton, University Road, Southampton, Hampshire SO17 1BJ UK
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Brügger A, Bilheux HZ, Lin JYY, Nelson GJ, Kiss AM, Morris J, Connolly MJ, Long AM, Tremsin AS, Strzelec A, Anderson MH, Agasie R, Finney CEA, Wissink ML, Hubler MH, Pellenq RJM, White CE, Heuser BJ, Craft AE, Harp JM, Tan C, Morris K, Junghans A, Sevanto S, Warren JM, Esteban Florez FL, Biris AS, Cekanova M, Kardjilov N, Schillinger B, Frost MJ, Vogel SC. The Complex, Unique, and Powerful Imaging Instrument for Dynamics (CUPI2D) at the Spallation Neutron Source (invited). THE REVIEW OF SCIENTIFIC INSTRUMENTS 2023; 94:2890223. [PMID: 37171234 DOI: 10.1063/5.0131778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/05/2023] [Indexed: 05/13/2023]
Abstract
The Oak Ridge National Laboratory is planning to build the Second Target Station (STS) at the Spallation Neutron Source (SNS). STS will host a suite of novel instruments that complement the First Target Station's beamline capabilities by offering an increased flux for cold neutrons and a broader wavelength bandwidth. A novel neutron imaging beamline, named the Complex, Unique, and Powerful Imaging Instrument for Dynamics (CUPI2D), is among the first eight instruments that will be commissioned at STS as part of the construction project. CUPI2D is designed for a broad range of neutron imaging scientific applications, such as energy storage and conversion (batteries and fuel cells), materials science and engineering (additive manufacturing, superalloys, and archaeometry), nuclear materials (novel cladding materials, nuclear fuel, and moderators), cementitious materials, biology/medical/dental applications (regenerative medicine and cancer), and life sciences (plant-soil interactions and nutrient dynamics). The innovation of this instrument lies in the utilization of a high flux of wavelength-separated cold neutrons to perform real time in situ neutron grating interferometry and Bragg edge imaging-with a wavelength resolution of δλ/λ ≈ 0.3%-simultaneously when required, across a broad range of length and time scales. This manuscript briefly describes the science enabled at CUPI2D based on its unique capabilities. The preliminary beamline performance, a design concept, and future development requirements are also presented.
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Affiliation(s)
- Adrian Brügger
- Civil Engineering & Engineering Mechanics, Columbia University, New York, New York 10027, USA
| | - Hassina Z Bilheux
- Oak Ridge National Laboratory, Spallation Neutron Source, Neutron Scattering Division, Oak Ridge, Tennessee 37831, USA
| | - Jiao Y Y Lin
- Oak Ridge National Laboratory, Second Target Station Project, Oak Ridge, Tennessee 37831, USA
| | - George J Nelson
- Mechanical and Aerospace Engineering, University of Alabama-Huntsville, Huntsville, Alabama 35899, USA
| | - Andrew M Kiss
- Brookhaven National Laboratory, National Synchrotron Light Source II, Photon Science Division, Upton, New York 11973, USA
| | | | - Matthew J Connolly
- Material Measurement Laboratory/Applied Chemicals and Materials Division, National Institute of Standards and Technology, Boulder, Colorado 80305, USA
| | - Alexander M Long
- Los Alamos National Laboratory, Materials Science and Technology Division, Los Alamos, New Mexico 87545, USA
| | - Anton S Tremsin
- Space Science Laboratory, University of California-Berkeley, Berkeley, California 94720, USA
| | - Andrea Strzelec
- College of Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Mark H Anderson
- College of Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Robert Agasie
- College of Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Charles E A Finney
- Oak Ridge National Laboratory, Buildings and Transportation Science Division, Oak Ridge, Tennessee 37831, USA
| | - Martin L Wissink
- Oak Ridge National Laboratory, Buildings and Transportation Science Division, Oak Ridge, Tennessee 37831, USA
| | - Mija H Hubler
- College of Engineering and Applied Science, University of Colorado-Boulder, Boulder, Colorado 80309, USA
| | - Roland J-M Pellenq
- International Research Laboratory, CNRS-George Washington University, Washington, District of Columbia 20052, USA
| | - Claire E White
- Civil and Environmental Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Brent J Heuser
- The Grainger College of Engineering, University of Illinois-Urbana Champaign, Urbana, Illinois 61801, USA
| | - Aaron E Craft
- Idaho National Laboratory, Characterization and Advanced Post-Irradiation Examination Division, Idaho Falls, Idaho 83415, USA
| | - Jason M Harp
- Oak Ridge National Laboratory, Nuclear Energy and Fuel Cycle Division, Oak Ridge, Tennessee 37831, USA
| | - Chuting Tan
- Idaho National Laboratory, Characterization and Advanced Post-Irradiation Examination Division, Idaho Falls, Idaho 83415, USA
| | | | - Ann Junghans
- Los Alamos National Laboratory, Nuclear Engineering and Nonproliferation Division, Los Alamos, New Mexico 87545, USA
| | - Sanna Sevanto
- Los Alamos National Laboratory, Environmental Sciences Division, Los Alamos, New Mexico 87545, USA
| | - Jeffrey M Warren
- Oak Ridge National Laboratory, Environmental Sciences Division, Oak Ridge, Tennessee 37831, USA
| | - Fernando L Esteban Florez
- University of Oklahoma Health Sciences Center College of Dentistry, Oklahoma City, Oklahoma 73117, USA
| | - Alexandru S Biris
- Center for Integrative Nanotechnology Sciences, University of Arkansas at Little Rock, Little Rock, Arkansas 72204, USA
| | - Maria Cekanova
- Integrity Laboratories, LLC, Knoxville, Tennessee 37932, USA
| | - Nikolay Kardjilov
- Helmholtz-Zentrum-Berlin, Institute Applied Materials, Berlin 14109, Germany
| | | | - Matthew J Frost
- Oak Ridge National Laboratory, Neutron Technologies Division, Oak Ridge, Tennessee 37831, USA
| | - Sven C Vogel
- Los Alamos National Laboratory, Materials Science and Technology Division, Los Alamos, New Mexico 87545, USA
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Kohli PS, Pazhamala LT, Mani B, Thakur JK, Giri J. Root hair-specific transcriptome reveals response to low phosphorus in Cicer arietinum. FRONTIERS IN PLANT SCIENCE 2022; 13:983969. [PMID: 36267945 PMCID: PMC9577374 DOI: 10.3389/fpls.2022.983969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/16/2022] [Indexed: 06/16/2023]
Abstract
Root hairs (RH) are a single-cell extension of root epidermal cells. In low phosphorus (LP) availability, RH length and density increase thus expanding the total root surface area for phosphate (Pi) acquisition. However, details on genes involved in RH development and response to LP are missing in an agronomically important leguminous crop, chickpea. To elucidate this response in chickpea, we performed tissue-specific RNA-sequencing and analyzed the transcriptome modulation for RH and root without RH (Root-RH) under LP. Root hair initiation and cellular differentiation genes like RSL TFs and ROPGEFs are upregulated in Root-RH, explaining denser, and ectopic RH in LP. In RH, genes involved in tip growth processes and phytohormonal biosynthesis like cell wall synthesis and loosening (cellulose synthase A catalytic subunit, CaEXPA2, CaGRP2, and CaXTH2), cytoskeleton/vesicle transport, and ethylene biosynthesis are upregulated. Besides RH development, genes involved in LP responses like lipid and/or pectin P remobilization and acid phosphatases are induced in these tissues summarizing a complete molecular response to LP. Further, RH displayed preferential enrichment of processes involved in symbiotic interactions, which provide an additional benefit during LP. In conclusion, RH shows a multi-faceted response that starts with molecular changes for epidermal cell differentiation and RH initiation in Root-RH and later induction of tip growth and various LP responses in elongated RH.
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Affiliation(s)
| | | | - Balaji Mani
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Jitendra Kumar Thakur
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
- International Center of Genetic Engineering and Biotechnology, New Delhi, India
| | - Jitender Giri
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
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Williams KA, McKay Fletcher DM, Petroselli C, Ruiz SA, Roose T. A 3D image-based modelling approach for understanding spatiotemporal processes in phosphorus fertiliser dissolution, soil buffering and uptake by plant roots. Sci Rep 2022; 12:15891. [PMID: 36151240 PMCID: PMC9508158 DOI: 10.1038/s41598-022-19047-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 08/23/2022] [Indexed: 11/18/2022] Open
Abstract
Phosphorus (P) is a key yield-limiting nutrient for crops, but the main source of P fertiliser is finite. Therefore, efficient fertilisation is crucial. Optimal P application requires understanding of the dynamic processes affecting P availability to plants, including fertiliser dissolution rate and soil buffer power. However, standard soil testing methods sample at fixed time points, preventing a mechanistic understanding of P uptake variability. We used image-based modelling to investigate the effects of fertiliser dissolution rate and soil buffer power on P uptake by wheat roots imaged using X-ray CT. We modelled uptake based on 1-day, 1-week, and 14-week dissolution of a fixed quantity of total P for two common soil buffer powers. We found rapid fertiliser dissolution increased short-term root uptake, but total uptake from 1-week matched 1-day dissolution. We quantified the large effects root system architecture had on P uptake, finding that there were trade-offs between total P uptake and uptake per unit root length, representing a carbon investment/phosphorus uptake balance. These results provide a starting point for predictive modelling of uptake from different P fertilisers in different soils. With the addition of further X-ray CT image datasets and a wider range of conditions, our simulation approach could be developed further for rapid trialling of fertiliser-soil combinations to inform field-scale trials or management.
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Affiliation(s)
- K A Williams
- Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UK.,Faculty of Science and Health, University of Portsmouth, Portsmouth, UK
| | - D M McKay Fletcher
- Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UK
| | - C Petroselli
- Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UK
| | - S A Ruiz
- Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UK
| | - T Roose
- Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UK.
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9
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Wheat genomic study for genetic improvement of traits in China. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1718-1775. [PMID: 36018491 DOI: 10.1007/s11427-022-2178-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/10/2022] [Indexed: 01/17/2023]
Abstract
Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.
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10
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Indore NS, Karunakaran C, Jayas DS. Synchrotron tomography applications in agriculture and food sciences research: a review. PLANT METHODS 2022; 18:101. [PMID: 35964094 PMCID: PMC9375343 DOI: 10.1186/s13007-022-00932-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/01/2022] [Indexed: 05/28/2023]
Abstract
Synchrotron imaging is widely used for research in many scientific disciplines. This article introduces the characteristics of synchrotron X-ray imaging and its applications in agriculture and food science research. The agriculture and food sector are a vast area that comprises of plants, seeds, animals, food and their products; soils with thriving microbial communities; and natural resources such as water, fertilizers, and organic matter. These entities have unique internal features, structures and compositions which differentiate them from each other in varieties, species, grades, and types. The use of a bright and tuneable monochromatic source of synchrotron imaging techniques enables researchers to study the internal features and compositions of plants, seeds, soil and food in a quick and non-destructive way to enhance their use, conservation and productivity. Synchrotron's different X-ray imaging techniques offer a wide domain of applications, which make them perfect to enhance the understanding of structures of raw and processed food products to promote food safety and security. Therefore, this paper summarizes the results of major experiments carried out with seeds, plants, soil, food and relevant areas of agricultural sciences with more emphasis on two synchrotron X-ray imaging techniques: absorption and phase-contrast imaging and computed tomography.
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Affiliation(s)
- Navnath S Indore
- Biosystem Engineering, University of Manitoba, Winnipeg, MB, R3T 5V6, Canada
| | - Chithra Karunakaran
- Biosystem Engineering, University of Manitoba, Winnipeg, MB, R3T 5V6, Canada
- Canadian Light Source Inc., Saskatoon, SK, S7N 2V3, Canada
| | - Digvir S Jayas
- Biosystem Engineering, University of Manitoba, Winnipeg, MB, R3T 5V6, Canada.
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11
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Hallett PD, Marin M, Bending GD, George TS, Collins CD, Otten W. Building soil sustainability from root-soil interface traits. TRENDS IN PLANT SCIENCE 2022; 27:688-698. [PMID: 35168900 DOI: 10.1016/j.tplants.2022.01.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 01/06/2022] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Great potential exists to harness plant traits at the root-soil interface, mainly rhizodeposition and root hairs, to 'build' soils with better structure that can trap more carbon and resources, resist climate stresses, and promote a healthy microbiome. These traits appear to have been preserved in modern crop varieties, but scope exists to improve them further because they vary considerably between genotypes and respond to environmental conditions. From emerging evidence, rhizodeposition can act as a disperser, aggregator, and/or hydrogel in soil, and root hairs expand rhizosheath size. Future research should explore impacts of selecting these traits on plants and soils concurrently, expanding from model plants to commercial genotypes, and observing whether impacts currently limited to glasshouse studies occur in the field.
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Affiliation(s)
- Paul D Hallett
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK.
| | - Maria Marin
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | - Gary D Bending
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Timothy S George
- Ecological Sciences Group, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Chris D Collins
- Department of Geography and Environmental Science, University of Reading, Reading RG6 6DW, UK
| | - Wilfred Otten
- Cranfield Soil and Agrifood Institute, College Road, Cranfield, MK43 0AL, UK
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12
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Duddek P, Carminati A, Koebernick N, Ohmann L, Lovric G, Delzon S, Rodriguez‐Dominguez CM, King A, Ahmed MA. The impact of drought-induced root and root hair shrinkage on root-soil contact. PLANT PHYSIOLOGY 2022; 189:1232-1236. [PMID: 35325215 PMCID: PMC9237671 DOI: 10.1093/plphys/kiac144] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/05/2022] [Indexed: 05/16/2023]
Abstract
Although root hairs significantly increased root–soil contact, in maize, their shrinkage during soil drying is initiated at relatively high soil matric potentials (between −10 and −310 kPa).
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Affiliation(s)
- Patrick Duddek
- Physics of Soils and Terrestrial Ecosystems, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Universitätsstrasse 16, 8092 Zurich, Switzerland
- Chair of Soil Physics, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Universitätstrasse 30, 95447 Bayreuth, Germany
| | - Andrea Carminati
- Physics of Soils and Terrestrial Ecosystems, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Universitätsstrasse 16, 8092 Zurich, Switzerland
| | - Nicolai Koebernick
- Soil Science and Soil Protection, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 3, 06120 Halle (Saale), Germany
| | - Luise Ohmann
- Department of Soil System Science, Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
| | - Goran Lovric
- Swiss Light Source, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Sylvain Delzon
- BIOGECO, INRA, Univ. Bordeaux, Allée Geoffroy St-Hilaire, 33615 Pessac, France
| | | | - Andrew King
- Synchrotron SOLEIL, L’Orme des Merisiers, 91192 Gif-sur-Yvette Cedex, France
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13
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De Pessemier J, Moturu TR, Nacry P, Ebert R, De Gernier H, Tillard P, Swarup K, Wells DM, Haseloff J, Murray SC, Bennett MJ, Inzé D, Vincent CI, Hermans C. Root system size and root hair length are key phenes for nitrate acquisition and biomass production across natural variation in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3569-3583. [PMID: 35304891 DOI: 10.1093/jxb/erac118] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
The role of root phenes in nitrogen (N) acquisition and biomass production was evaluated in 10 contrasting natural accessions of Arabidopsis thaliana L. Seedlings were grown on vertical agar plates with two different nitrate supplies. The low N treatment increased the root to shoot biomass ratio and promoted the proliferation of lateral roots and root hairs. The cost of a larger root system did not impact shoot biomass. Greater biomass production could be achieved through increased root length or through specific root hair characteristics. A greater number of root hairs may provide a low-resistance pathway under elevated N conditions, while root hair length may enhance root zone exploration under low N conditions. The variability of N uptake and the expression levels of genes encoding nitrate transporters were measured. A positive correlation was found between root system size and high-affinity nitrate uptake, emphasizing the benefits of an exploratory root organ in N acquisition. The expression levels of NRT1.2/NPF4.6, NRT2.2, and NRT1.5/NPF7.3 negatively correlated with some root morphological traits. Such basic knowledge in Arabidopsis demonstrates the importance of root phenes to improve N acquisition and paves the way to design eudicot ideotypes.
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Affiliation(s)
- Jérôme De Pessemier
- Crop Production and Biostimulation Laboratory, Interfacultary School of Bioengineers, Université libre de Bruxelles, B-1050 Brussels, Belgium
| | - Taraka Ramji Moturu
- Crop Production and Biostimulation Laboratory, Interfacultary School of Bioengineers, Université libre de Bruxelles, B-1050 Brussels, Belgium
| | - Philippe Nacry
- Institute of Plant Science Montpellier, Université de Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
| | - Rebecca Ebert
- Citrus Research and Education Center, Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Hugues De Gernier
- Crop Production and Biostimulation Laboratory, Interfacultary School of Bioengineers, Université libre de Bruxelles, B-1050 Brussels, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Pascal Tillard
- Institute of Plant Science Montpellier, Université de Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
| | - Kamal Swarup
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Darren M Wells
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Seth C Murray
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Malcolm J Bennett
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Christopher I Vincent
- Citrus Research and Education Center, Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Christian Hermans
- Crop Production and Biostimulation Laboratory, Interfacultary School of Bioengineers, Université libre de Bruxelles, B-1050 Brussels, Belgium
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14
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Vincent C, Ebert R, Hermans C. Root hair quantification is an accessible approach to phenotyping important functional traits. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3304-3307. [PMID: 35290442 DOI: 10.1093/jxb/erac102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Christopher Vincent
- Citrus Research and Education Center, Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Rebecca Ebert
- Citrus Research and Education Center, Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Christian Hermans
- Crop Production and Biostimulation Laboratory, Université libre de Bruxelles, B-1050 Brussels, Belgium
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15
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Kohli PS, Maurya K, Thakur JK, Bhosale R, Giri J. Significance of root hairs in developing stress-resilient plants for sustainable crop production. PLANT, CELL & ENVIRONMENT 2022; 45:677-694. [PMID: 34854103 DOI: 10.1111/pce.14237] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 11/15/2021] [Accepted: 11/21/2021] [Indexed: 06/13/2023]
Abstract
Root hairs represent a beneficial agronomic trait to potentially reduce fertilizer and irrigation inputs. Over the past decades, research in the plant model Arabidopsis thaliana has provided insights into root hair development, the underlying genetic framework and the integration of environmental cues within this framework. Recent years have seen a paradigm shift, where studies are now highlighting conservation and diversification of root hair developmental programs in other plant species and the agronomic relevance of root hairs in a wider ecological context. In this review, we specifically discuss the molecular evolution of the RSL (RHD Six-Like) pathway that controls root hair development and growth in land plants. We also discuss how root hairs contribute to plant performance as an active physiological rooting structure by performing resource acquisition, providing anchorage and constructing the rhizosphere with desirable physical, chemical and biological properties. Finally, we outline future research directions that can help achieve the potential of root hairs in developing sustainable agroecosystems.
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Affiliation(s)
| | - Kanika Maurya
- National Institute of Plant Genome Research, New Delhi, India
| | - Jitendra K Thakur
- National Institute of Plant Genome Research, New Delhi, India
- International Centre of Genetic Engineering and Biotechnology, New Delhi, India
| | - Rahul Bhosale
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, Nottingham, UK
| | - Jitender Giri
- National Institute of Plant Genome Research, New Delhi, India
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16
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Freschet GT, Pagès L, Iversen CM, Comas LH, Rewald B, Roumet C, Klimešová J, Zadworny M, Poorter H, Postma JA, Adams TS, Bagniewska‐Zadworna A, Bengough AG, Blancaflor EB, Brunner I, Cornelissen JHC, Garnier E, Gessler A, Hobbie SE, Meier IC, Mommer L, Picon‐Cochard C, Rose L, Ryser P, Scherer‐Lorenzen M, Soudzilovskaia NA, Stokes A, Sun T, Valverde‐Barrantes OJ, Weemstra M, Weigelt A, Wurzburger N, York LM, Batterman SA, Gomes de Moraes M, Janeček Š, Lambers H, Salmon V, Tharayil N, McCormack ML. A starting guide to root ecology: strengthening ecological concepts and standardising root classification, sampling, processing and trait measurements. THE NEW PHYTOLOGIST 2021; 232:973-1122. [PMID: 34608637 PMCID: PMC8518129 DOI: 10.1111/nph.17572] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/22/2021] [Indexed: 05/17/2023]
Abstract
In the context of a recent massive increase in research on plant root functions and their impact on the environment, root ecologists currently face many important challenges to keep on generating cutting-edge, meaningful and integrated knowledge. Consideration of the below-ground components in plant and ecosystem studies has been consistently called for in recent decades, but methodology is disparate and sometimes inappropriate. This handbook, based on the collective effort of a large team of experts, will improve trait comparisons across studies and integration of information across databases by providing standardised methods and controlled vocabularies. It is meant to be used not only as starting point by students and scientists who desire working on below-ground ecosystems, but also by experts for consolidating and broadening their views on multiple aspects of root ecology. Beyond the classical compilation of measurement protocols, we have synthesised recommendations from the literature to provide key background knowledge useful for: (1) defining below-ground plant entities and giving keys for their meaningful dissection, classification and naming beyond the classical fine-root vs coarse-root approach; (2) considering the specificity of root research to produce sound laboratory and field data; (3) describing typical, but overlooked steps for studying roots (e.g. root handling, cleaning and storage); and (4) gathering metadata necessary for the interpretation of results and their reuse. Most importantly, all root traits have been introduced with some degree of ecological context that will be a foundation for understanding their ecological meaning, their typical use and uncertainties, and some methodological and conceptual perspectives for future research. Considering all of this, we urge readers not to solely extract protocol recommendations for trait measurements from this work, but to take a moment to read and reflect on the extensive information contained in this broader guide to root ecology, including sections I-VII and the many introductions to each section and root trait description. Finally, it is critical to understand that a major aim of this guide is to help break down barriers between the many subdisciplines of root ecology and ecophysiology, broaden researchers' views on the multiple aspects of root study and create favourable conditions for the inception of comprehensive experiments on the role of roots in plant and ecosystem functioning.
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Affiliation(s)
- Grégoire T. Freschet
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
- Station d’Ecologie Théorique et ExpérimentaleCNRS2 route du CNRS09200MoulisFrance
| | - Loïc Pagès
- UR 1115 PSHCentre PACA, site AgroparcINRAE84914Avignon cedex 9France
| | - Colleen M. Iversen
- Environmental Sciences Division and Climate Change Science InstituteOak Ridge National LaboratoryOak RidgeTN37831USA
| | - Louise H. Comas
- USDA‐ARS Water Management Research Unit2150 Centre Avenue, Bldg D, Suite 320Fort CollinsCO80526USA
| | - Boris Rewald
- Department of Forest and Soil SciencesUniversity of Natural Resources and Life SciencesVienna1190Austria
| | - Catherine Roumet
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
| | - Jitka Klimešová
- Department of Functional EcologyInstitute of Botany CASDukelska 13537901TrebonCzech Republic
| | - Marcin Zadworny
- Institute of DendrologyPolish Academy of SciencesParkowa 562‐035KórnikPoland
| | - Hendrik Poorter
- Plant Sciences (IBG‐2)Forschungszentrum Jülich GmbHD‐52425JülichGermany
- Department of Biological SciencesMacquarie UniversityNorth RydeNSW2109Australia
| | | | - Thomas S. Adams
- Department of Plant SciencesThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Agnieszka Bagniewska‐Zadworna
- Department of General BotanyInstitute of Experimental BiologyFaculty of BiologyAdam Mickiewicz UniversityUniwersytetu Poznańskiego 661-614PoznańPoland
| | - A. Glyn Bengough
- The James Hutton InstituteInvergowrie, Dundee,DD2 5DAUK
- School of Science and EngineeringUniversity of DundeeDundee,DD1 4HNUK
| | | | - Ivano Brunner
- Forest Soils and BiogeochemistrySwiss Federal Research Institute WSLZürcherstr. 1118903BirmensdorfSwitzerland
| | - Johannes H. C. Cornelissen
- Department of Ecological ScienceFaculty of ScienceVrije Universiteit AmsterdamDe Boelelaan 1085Amsterdam1081 HVthe Netherlands
| | - Eric Garnier
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
| | - Arthur Gessler
- Forest DynamicsSwiss Federal Research Institute WSLZürcherstr. 1118903BirmensdorfSwitzerland
- Institute of Terrestrial EcosystemsETH Zurich8092ZurichSwitzerland
| | - Sarah E. Hobbie
- Department of Ecology, Evolution and BehaviorUniversity of MinnesotaSt PaulMN55108USA
| | - Ina C. Meier
- Functional Forest EcologyUniversity of HamburgHaidkrugsweg 122885BarsbütelGermany
| | - Liesje Mommer
- Plant Ecology and Nature Conservation GroupDepartment of Environmental SciencesWageningen University and ResearchPO Box 476700 AAWageningenthe Netherlands
| | | | - Laura Rose
- Station d’Ecologie Théorique et ExpérimentaleCNRS2 route du CNRS09200MoulisFrance
- Senckenberg Biodiversity and Climate Research Centre (BiK-F)Senckenberganlage 2560325Frankfurt am MainGermany
| | - Peter Ryser
- Laurentian University935 Ramsey Lake RoadSudburyONP3E 2C6Canada
| | | | - Nadejda A. Soudzilovskaia
- Environmental Biology DepartmentInstitute of Environmental SciencesCMLLeiden UniversityLeiden2300 RAthe Netherlands
| | - Alexia Stokes
- INRAEAMAPCIRAD, IRDCNRSUniversity of MontpellierMontpellier34000France
| | - Tao Sun
- Institute of Applied EcologyChinese Academy of SciencesShenyang110016China
| | - Oscar J. Valverde‐Barrantes
- International Center for Tropical BotanyDepartment of Biological SciencesFlorida International UniversityMiamiFL33199USA
| | - Monique Weemstra
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
| | - Alexandra Weigelt
- Systematic Botany and Functional BiodiversityInstitute of BiologyLeipzig UniversityJohannisallee 21-23Leipzig04103Germany
| | - Nina Wurzburger
- Odum School of EcologyUniversity of Georgia140 E. Green StreetAthensGA30602USA
| | - Larry M. York
- Biosciences Division and Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTN37831USA
| | - Sarah A. Batterman
- School of Geography and Priestley International Centre for ClimateUniversity of LeedsLeedsLS2 9JTUK
- Cary Institute of Ecosystem StudiesMillbrookNY12545USA
| | - Moemy Gomes de Moraes
- Department of BotanyInstitute of Biological SciencesFederal University of Goiás1974690-900Goiânia, GoiásBrazil
| | - Štěpán Janeček
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawley (Perth)WA 6009Australia
| | - Hans Lambers
- School of Biological SciencesThe University of Western AustraliaCrawley (Perth)WAAustralia
| | - Verity Salmon
- Environmental Sciences Division and Climate Change Science InstituteOak Ridge National LaboratoryOak RidgeTN37831USA
| | - Nishanth Tharayil
- Department of Plant and Environmental SciencesClemson UniversityClemsonSC29634USA
| | - M. Luke McCormack
- Center for Tree ScienceMorton Arboretum, 4100 Illinois Rt. 53LisleIL60532USA
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17
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Piovesan A, Vancauwenberghe V, Van De Looverbosch T, Verboven P, Nicolaï B. X-ray computed tomography for 3D plant imaging. TRENDS IN PLANT SCIENCE 2021; 26:1171-1185. [PMID: 34404587 DOI: 10.1016/j.tplants.2021.07.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/05/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
X-ray computed tomography (CT) is a valuable tool for 3D imaging of plant tissues and organs. Applications include the study of plant development and organ morphogenesis, as well as modeling of transport processes in plants. Some challenges remain, however, including attaining higher contrast for easier quantification, increasing the resolution for imaging subcellular features, and decreasing image acquisition and processing time for high-throughput phenotyping. In addition, phase contrast, multispectral, dark-field, soft X-ray, and time-resolved imaging are emerging. At the same time, a large amount of 3D image data are becoming available, posing challenges for data management. We review recent advances in the area of X-ray CT for plant imaging, and describe opportunities for using such images for studying transport processes in plants.
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Affiliation(s)
- Agnese Piovesan
- Katholieke Universiteit (KU) Leuven, Division MeBioS (Mechatronics, Biostatistics, and Sensors) - Postharvest Group, Willem de Croylaan 42, BE-3001 Leuven, Belgium
| | - Valérie Vancauwenberghe
- Katholieke Universiteit (KU) Leuven, Division MeBioS (Mechatronics, Biostatistics, and Sensors) - Postharvest Group, Willem de Croylaan 42, BE-3001 Leuven, Belgium
| | - Tim Van De Looverbosch
- Katholieke Universiteit (KU) Leuven, Division MeBioS (Mechatronics, Biostatistics, and Sensors) - Postharvest Group, Willem de Croylaan 42, BE-3001 Leuven, Belgium
| | - Pieter Verboven
- Katholieke Universiteit (KU) Leuven, Division MeBioS (Mechatronics, Biostatistics, and Sensors) - Postharvest Group, Willem de Croylaan 42, BE-3001 Leuven, Belgium.
| | - Bart Nicolaï
- Katholieke Universiteit (KU) Leuven, Division MeBioS (Mechatronics, Biostatistics, and Sensors) - Postharvest Group, Willem de Croylaan 42, BE-3001 Leuven, Belgium; Flanders Centre of Postharvest Technology (VCBT), Willem de Croylaan 42, BE-3001 Leuven, Belgium
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18
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Strandberg A, Skoglund N, Thyrel M. Morphological characterisation of ash particles from co-combustion of sewage sludge and wheat straw with X-ray microtomography. WASTE MANAGEMENT (NEW YORK, N.Y.) 2021; 135:30-39. [PMID: 34461488 DOI: 10.1016/j.wasman.2021.08.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 08/04/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
Combustion of phosphorus-rich residual streams can produce nutrient-rich ashes and these can be used either in further processing or as materials for direct nutrient recycling. The latter requires knowledge on morphological parameters of such ash particles that may impact plant growth, nutrient availability, and soil physical properties. The present work aims to determine the porosity, pore size, and specific surface area of ash particles, and discuss these properties in light of literature concerning interaction with soil water and plant roots. Bottom ash particles from combustion of sewage sludge and wheat straw and their co-combustion were analysed with X-ray microtomography. Image analysis provided information on morphology, specific surface area, porosity, and pore structure on a micrometre scale resolution. Co-combusting sewage sludge with wheat straw resulted in differences in ash particles' porosity and pore structure compared to combustion of pure fuels. Pure wheat straw ash displayed 62 vol% porosity while there was no apparent difference between 10 wt% or 30 wt% mixtures of sewage sludge, with a porosity of 29-31 vol%. Open pore volume comprise the largest part of the porosity (72-99 vol%) enabling interaction between surrounding pore water and nutrients. Overall, the ash particles display large open volume fractions and thin particle walls which may lead to rapid weathering and extensive interaction with soil water. The particles generally contained pore openings over 200 µm towards the surroundings, which provide opportunities for interaction with microbes and roots from a variety of plant species in addition to nutrient transport by soil water.
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Affiliation(s)
- Anna Strandberg
- Swedish University of Agricultural Sciences, Department of Forest Biomaterials and Technology, SE 901 83 Umeå, Sweden; Umeå University, Department of Applied Physics and Electronics, Thermochemical Energy Conversion Laboratory, SE 901 87 Umeå, Sweden.
| | - Nils Skoglund
- Umeå University, Department of Applied Physics and Electronics, Thermochemical Energy Conversion Laboratory, SE 901 87 Umeå, Sweden.
| | - Mikael Thyrel
- Swedish University of Agricultural Sciences, Department of Forest Biomaterials and Technology, SE 901 83 Umeå, Sweden.
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19
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Liu S, Barrow CS, Hanlon M, Lynch JP, Bucksch A. DIRT/3D: 3D root phenotyping for field-grown maize (Zea mays). PLANT PHYSIOLOGY 2021; 187:739-757. [PMID: 34608967 PMCID: PMC8491025 DOI: 10.1093/plphys/kiab311] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 06/09/2021] [Indexed: 05/25/2023]
Abstract
The development of crops with deeper roots holds substantial promise to mitigate the consequences of climate change. Deeper roots are an essential factor to improve water uptake as a way to enhance crop resilience to drought, to increase nitrogen capture, to reduce fertilizer inputs, and to increase carbon sequestration from the atmosphere to improve soil organic fertility. A major bottleneck to achieving these improvements is high-throughput phenotyping to quantify root phenotypes of field-grown roots. We address this bottleneck with Digital Imaging of Root Traits (DIRT)/3D, an image-based 3D root phenotyping platform, which measures 18 architecture traits from mature field-grown maize (Zea mays) root crowns (RCs) excavated with the Shovelomics technique. DIRT/3D reliably computed all 18 traits, including distance between whorls and the number, angles, and diameters of nodal roots, on a test panel of 12 contrasting maize genotypes. The computed results were validated through comparison with manual measurements. Overall, we observed a coefficient of determination of r2>0.84 and a high broad-sense heritability of Hmean2> 0.6 for all but one trait. The average values of the 18 traits and a developed descriptor to characterize complete root architecture distinguished all genotypes. DIRT/3D is a step toward automated quantification of highly occluded maize RCs. Therefore, DIRT/3D supports breeders and root biologists in improving carbon sequestration and food security in the face of the adverse effects of climate change.
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Affiliation(s)
- Suxing Liu
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia 30602, USA
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, USA
| | | | - Meredith Hanlon
- Department of Plant Science, Pennsylvania State University, State College, Pennsylvania 16802, USA
| | - Jonathan P. Lynch
- Department of Plant Science, Pennsylvania State University, State College, Pennsylvania 16802, USA
| | - Alexander Bucksch
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia 30602, USA
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, USA
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20
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Haber-Pohlmeier S, Caterina D, Blümich B, Pohlmeier A. Magnetic Resonance Imaging of Water Content and Flow Processes in Natural Soils by Pulse Sequences with Ultrashort Detection. Molecules 2021; 26:molecules26175130. [PMID: 34500563 PMCID: PMC8433766 DOI: 10.3390/molecules26175130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 11/17/2022] Open
Abstract
Magnetic resonance imaging is a valuable tool for three-dimensional mapping of soil water processes due to its sensitivity to the substance of interest: water. Since conventional gradient- or spin-echo based pulse sequences do not detect rapidly relaxing fractions of water in natural porous media with transverse relaxation times in the millisecond range, pulse sequences with ultrafast detection open a way out. In this work, we compare a spin-echo multislice pulse sequence with ultrashort (UTE) and zero-TE (ZTE) sequences for their suitability to map water content and its changes in 3D in natural soil materials. Longitudinal and transverse relaxation times were found in the ranges around 80 ms and 1 to 50 ms, respectively, so that the spin echo sequence misses larger fractions of water. In contrast, ZTE and UTE could detect all water, if the excitation and detection bandwidths were set sufficiently broad. More precisely, with ZTE we could map water contents down to 0.1 cm3/cm3. Finally, we employed ZTE to monitor the development of film flow in a natural soil core with high temporal resolution. This opens the route for further quantitative imaging of soil water processes.
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Affiliation(s)
- Sabina Haber-Pohlmeier
- Institute for Modelling Hydraulic and Environmental Systems, University of Stuttgart, Pfaffenwaldring 61, D-70569 Stuttgart, Germany;
| | - David Caterina
- Institute for Bio- and Geosciences Agrosphere (IBG-3), Research Center Jülich, D-52425 Jülich, Germany;
- Département UEE, Faculté des Sciences Appliquées, Université de Liège, B-4000 Liège, Belgium
| | - Bernhard Blümich
- Institute for Technical and Macromolecular Chemistry, RWTH Aachen University, Worringer Weg 2, D-52074 Aachen, Germany;
| | - Andreas Pohlmeier
- Institute for Bio- and Geosciences Agrosphere (IBG-3), Research Center Jülich, D-52425 Jülich, Germany;
- Correspondence:
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21
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Scotson CP, van Veelen A, Williams KA, Koebernick N, McKay Fletcher D, Roose T. Developing a system for in vivo imaging of maize roots containing iodinated contrast media in soil using synchrotron XCT and XRF. PLANT AND SOIL 2020; 460:647-665. [PMID: 34720206 PMCID: PMC8550435 DOI: 10.1007/s11104-020-04784-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 11/25/2020] [Indexed: 06/13/2023]
Abstract
AIMS We sought to develop a novel experimental system which enabled application of iodinated contrast media to in vivo plant roots intact in soil and was compatible with time-resolved synchrotron X-ray computed tomography imaging. The system was developed to overcome issues of low contrast to noise within X-ray computed tomography images of plant roots and soil environments, the latter of which can complicate image processing and result in the loss of anatomical information. METHODS To demonstrate the efficacy of the system we employ the novel use of both synchrotron X-ray computed tomography and synchrotron X-ray fluorescence mapping to capture the translocation of the contrast media through root vasculature into the leaves. RESULTS With the application of contrast media we identify fluid flow in root vasculature and visualise anatomical features, which are otherwise often only observable in ex vivo microscopy, including: the xylem, metaxylem, pith, fibres in aerenchyma and leaf venation. We are also able to observe interactions between aerenchyma cross sectional area and solute transport in the root vasculature with depth. CONCLUSIONS Our novel system was capable of successfully delivering sufficient contrast media into root and leaf tissues such that anatomical features could be visualised and internal fluid transport observed. We propose that our system could be used in future to study internal plant transport mechanisms and parameterise models for fluid flow in plants. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11104-020-04784-x.
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Affiliation(s)
- Callum P. Scotson
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, University Road, Southampton, SO17 1BJ UK
| | - Arjen van Veelen
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, University Road, Southampton, SO17 1BJ UK
- Material Science and Technology Division, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Katherine A. Williams
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, University Road, Southampton, SO17 1BJ UK
| | - Nicolai Koebernick
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, University Road, Southampton, SO17 1BJ UK
- Soil Science and Soil Protection, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 3, 06120 Halle (Saale), Germany
| | - Dan McKay Fletcher
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, University Road, Southampton, SO17 1BJ UK
| | - Tiina Roose
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, University Road, Southampton, SO17 1BJ UK
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Khalil AM, Murchie EH, Mooney SJ. Quantifying the influence of water deficit on root and shoot growth in wheat using X-ray Computed Tomography. AOB PLANTS 2020; 12:plaa036. [PMID: 32905427 PMCID: PMC7469715 DOI: 10.1093/aobpla/plaa036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 07/21/2020] [Indexed: 06/11/2023]
Abstract
The potential increased frequency and severity of drought associated with environmental change represents a significant obstacle to efforts aimed at enhancing food security due to its impact on crop development, and ultimately, yield. Our understanding of the impact of drought on crop growth in terms of plant aerial tissues is much more advanced than knowledge of the below-ground impacts. We undertook an experiment using X-ray Computed Tomography that aimed to support measurements of infrared gas exchange from plant shoots with quantification of 3D root architecture traits and the associated soil structural characteristics. Winter wheat (cv. Zebedee) was assessed at two early growth stages (14 and 21 days) under four water treatments (100, 75, 50 and 25 % of a notional field capacity (FC) and across two soil types (sandy loam and clay loam)). Plants generally grew better (to a larger size) in sandy loam soil as opposed to clay loam soil, most likely due to the soil structure and the associated pore network. All plants grew poorly under extreme water stress and displayed optimal growth at 75 % of FC, as opposed to 100 %, as the latter was most likely too wet. The optimal matric potential for root and shoot growth, inferred from the water release curve for each soil type, was higher than that for photosynthesis, stomatal conductance and transpiration suggesting root and shoot growth was more affected by soil water content than photosynthesis-related characteristics under water deficit conditions. With incidences of drought likely to increase, identification of wheat cultivars that are more tolerant of these conditions is important. Studies that consider the impact of water stress on both plant shoots and roots, and the role of the soil pore system such as this offer considerable potential in supporting these efforts.
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Affiliation(s)
- A M Khalil
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire, UK
- College of Agriculture, University of Duhok, Duhok–Kurdistan Region, Iraq
| | - E H Murchie
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire, UK
| | - S J Mooney
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire, UK
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Zhang H, Wang S, Ou Z. Analytical solutions of citrate–phosphate coupled model of rice (Oryza sativa L.) roots. INT J BIOMATH 2020. [DOI: 10.1142/s1793524520500618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The citrate secreted by the rice (Oryza sativa L.) roots will promote the absorption of phosphate, and this process is described by the Kirk model. In our work, the Kirk model is divided into citrate sub-model and phosphate sub-model. In the citrate sub-model, we obtain the analytical solution of citrate with the Laplace transform, inverse Laplace transform and convolution theorem. The citrate solution is substituted into the phosphate sub-model, and the analytical solution of phosphate is obtained by the separation variable method. The existence of the solutions can be proved by the comparison test, the Weierstrass M-test and the Abel discriminating method.
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Affiliation(s)
- Huiping Zhang
- School of Mathematics and Finance, Putian University, Putian, Fujian, P. R. China
| | - Shuyue Wang
- School of Mathematics and Information, Fujian Normal University, Fuzhou, Fujian, P. R. China
| | - Zhonghui Ou
- School of Mathematics and Information, Fujian Normal University, Fuzhou, Fujian, P. R. China
- Fujian Key Laboratory of Mathematical Analysis and Applications (FJKLMAA), Fujian Normal University, Fuzhou, Fujian, P. R. China
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Ruiz SA, McKay Fletcher DM, Boghi A, Williams KA, Duncan SJ, Scotson CP, Petroselli C, Dias TGS, Chadwick DR, Jones DL, Roose T. Image-based quantification of soil microbial dead zones induced by nitrogen fertilization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 727:138197. [PMID: 32498200 DOI: 10.1016/j.scitotenv.2020.138197] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/23/2020] [Accepted: 03/23/2020] [Indexed: 06/11/2023]
Abstract
Microbial communities in agricultural soils underpin many ecosystem services including the maintenance of soil structure, food production, water purification and carbon storage. However, the impact of fertilization on the health of microbial communities is not well understood. This study investigates the spatial and temporal dynamics of nitrogen (N) transport away from a fertilizer granule with pore scale resolution. Specifically, we examined how soil structure and moisture content influence fertilizer derived N movement through the soil pore network and the subsequent impact of on soil microbial communities. We develop a mathematical model to describe N transport and reactions in soil at the pore-scale. Using X-ray Computed Tomography scans, we reconstructed a microscale description of a soil-pore geometry as a computational mesh. Solving two-phase water/air model produced pore-scale water distributions at 15, 30 and 70% water-filled pore volume. The N-speciation model considered ammonium (NH4+), nitrate (NO3-) and dissolved organic N (DON), and included N immobilization, ammonification and nitrification processes, as well as diffusion in soil solution. We simulated the dissolution of a fertilizer pellet and a pore scale N cycle at three different water saturations. To aid interpretation of the model results, microbial activity at a range of N concentrations was measured. The model showed that the diffusion and concentration of N in water films is critically dependent upon soil moisture and N species. We predict that the maximum NH4+ and NO3- concentrations in soil solution around the pellet under dry conditions are in the order of 1 × 103 and 1 × 104 mol m-3 respectively, and under wet conditions 2 × 102 and 1 × 103 mol m-3, respectively. Supporting experimental evidence suggests that these concentrations would be sufficient to reduce microbial activity in the short-term in the zone immediately around the fertilizer pellet (ranging from 0.9 to 3.8 mm), causing a major loss of soil biological functioning. This model demonstrates the importance of pore-scale processes in regulating N movement and their interactions with the soil microbiome.
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Affiliation(s)
- S A Ruiz
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - D M McKay Fletcher
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - A Boghi
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, UK; Computational Science Ltd, 30a Bedford Place, Southampton SO15 2DG, UK
| | - K A Williams
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - S J Duncan
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - C P Scotson
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - C Petroselli
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - T G S Dias
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - D R Chadwick
- School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK; Interdisciplinary Research Centre for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing, China
| | - D L Jones
- School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK; SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - T Roose
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, UK.
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Calleja-Cabrera J, Boter M, Oñate-Sánchez L, Pernas M. Root Growth Adaptation to Climate Change in Crops. FRONTIERS IN PLANT SCIENCE 2020; 11:544. [PMID: 32457782 PMCID: PMC7227386 DOI: 10.3389/fpls.2020.00544] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 04/09/2020] [Indexed: 05/05/2023]
Abstract
Climate change is threatening crop productivity worldwide and new solutions to adapt crops to these environmental changes are urgently needed. Elevated temperatures driven by climate change affect developmental and physiological plant processes that, ultimately, impact on crop yield and quality. Plant roots are responsible for water and nutrients uptake, but changes in soil temperatures alters this process limiting crop growth. With the predicted variable climatic forecast, the development of an efficient root system better adapted to changing soil and environmental conditions is crucial for enhancing crop productivity. Root traits associated with improved adaptation to rising temperatures are increasingly being analyzed to obtain more suitable crop varieties. In this review, we will summarize the current knowledge about the effect of increasing temperatures on root growth and their impact on crop yield. First, we will describe the main alterations in root architecture that different crops undergo in response to warmer soils. Then, we will outline the main coordinated physiological and metabolic changes taking place in roots and aerial parts that modulate the global response of the plant to increased temperatures. We will discuss on some of the main regulatory mechanisms controlling root adaptation to warmer soils, including the activation of heat and oxidative pathways to prevent damage of root cells and disruption of root growth; the interplay between hormonal regulatory pathways and the global changes on gene expression and protein homeostasis. We will also consider that in the field, increasing temperatures are usually associated with other abiotic and biotic stresses such as drought, salinity, nutrient deficiencies, and pathogen infections. We will present recent advances on how the root system is able to integrate and respond to complex and different stimuli in order to adapt to an increasingly changing environment. Finally, we will discuss the new prospects and challenges in this field as well as the more promising pathways for future research.
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Affiliation(s)
| | | | | | - M. Pernas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
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Ruiz S, Koebernick N, Duncan S, Fletcher DM, Scotson C, Boghi A, Marin M, Bengough AG, George TS, Brown LK, Hallett PD, Roose T. Significance of root hairs at the field scale - modelling root water and phosphorus uptake under different field conditions. PLANT AND SOIL 2019; 447:281-304. [PMID: 32214504 PMCID: PMC7062663 DOI: 10.1007/s11104-019-04308-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 09/13/2019] [Indexed: 05/22/2023]
Abstract
ABSTRACT BACKGROUND AND AIMS Root hairs play a significant role in phosphorus (P) extraction at the pore scale. However, their importance at the field scale remains poorly understood. METHODS This study uses a continuum model to explore the impact of root hairs on the large-scale uptake of P, comparing root hair influence under different agricultural scenarios. High vs low and constant vs decaying P concentrations down the soil profile are considered, along with early vs late precipitation scenarios. RESULTS Simulation results suggest root hairs accounted for 50% of total P uptake by plants. Furthermore, a delayed initiation time of precipitation potentially limits the P uptake rate by over 50% depending on the growth period. Despite the large differences in the uptake rate, changes in the soil P concentration in the domain due to root solute uptake remains marginal when considering a single growth season. However, over the duration of 6 years, simulation results showed that noticeable differences arise over time. CONCLUSION Root hairs are critical to P capture, with uptake efficiency potentially enhanced by coordinating irrigation with P application during earlier growth stages of crops.
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Affiliation(s)
- S Ruiz
- 1Bioengineering Science Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Science, University of Southampton, Southampton, SO17 1BJ UK
| | - N Koebernick
- 1Bioengineering Science Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Science, University of Southampton, Southampton, SO17 1BJ UK
- 5Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Universitaetplatz 10, 06108 Halle (Saale), Germany
| | - S Duncan
- 1Bioengineering Science Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Science, University of Southampton, Southampton, SO17 1BJ UK
| | - D McKay Fletcher
- 1Bioengineering Science Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Science, University of Southampton, Southampton, SO17 1BJ UK
| | - C Scotson
- 1Bioengineering Science Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Science, University of Southampton, Southampton, SO17 1BJ UK
| | - A Boghi
- 1Bioengineering Science Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Science, University of Southampton, Southampton, SO17 1BJ UK
| | - M Marin
- 2School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU UK
| | - A G Bengough
- 3Ecological Sciences Group, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
- 4School of Science and Engineering, University of Dundee, Dundee, DD1 4HN UK
| | - T S George
- 3Ecological Sciences Group, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
| | - L K Brown
- 3Ecological Sciences Group, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
| | - P D Hallett
- 2School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU UK
| | - T Roose
- 1Bioengineering Science Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Science, University of Southampton, Southampton, SO17 1BJ UK
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McKay Fletcher DM, Shaw R, Sánchez-Rodríguez AR, Daly KR, van Veelen A, Jones DL, Roose T. Quantifying citrate-enhanced phosphate root uptake using microdialysis. PLANT AND SOIL 2019; 461:69-89. [PMID: 34720207 PMCID: PMC8550755 DOI: 10.1007/s11104-019-04376-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/13/2019] [Indexed: 06/13/2023]
Abstract
AIMS Organic acid exudation by plant roots is thought to promote phosphate (P) solubilisation and bioavailability in soils with poorly available nutrients. Here we describe a new combined experimental (microdialysis) and modelling approach to quantify citrate-enhanced P desorption and its importance for root P uptake. METHODS To mimic the rhizosphere, microdialysis probes were placed in soil and perfused with citrate solutions (0.1, 1.0 and 10 mM) and the amount of P recovered from soil used to quantify rhizosphere P availability. Parameters in a mathematical model describing probe P uptake, citrate exudation, P movement and citrate-enhanced desorption were fit to the experimental data. These parameters were used in a model of a root which exuded citrate and absorbed P. The importance of soil citrate-P mobilisation for root P uptake was then quantified using this model. RESULTS A plant needs to exude citrate at a rate of 0.73 μmol cm-1 of root h-1 to see a significant increase in P absorption. Microdialysis probes with citrate in the perfusate were shown to absorb similar quantities of P to an exuding root. CONCLUSION A single root exuding citrate at a typical rate (4.3 × 10-5 μmol m-1 of root h-1) did not contribute significantly to P uptake. Microdialysis probes show promise for measuring rhizosphere processes when calibration experiments and mathematical modelling are used to decouple microdialysis and rhizosphere mechanisms.
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Affiliation(s)
- D. M. McKay Fletcher
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering Sciences, Faculty of Engineering and Physical Sciences, University of Southampton, University Road, Southampton, SO17 1BJ UK
| | - R. Shaw
- Environment Centre Wales, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2UW UK
| | - A. R. Sánchez-Rodríguez
- Environment Centre Wales, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2UW UK
- Agronomy Department, University of Córdoba, Campus de Rabanales. Edificio C4 Celestino Mutis, 14071 Córdoba, Spain
| | - K. R. Daly
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering Sciences, Faculty of Engineering and Physical Sciences, University of Southampton, University Road, Southampton, SO17 1BJ UK
| | - A. van Veelen
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering Sciences, Faculty of Engineering and Physical Sciences, University of Southampton, University Road, Southampton, SO17 1BJ UK
| | - D. L. Jones
- Environment Centre Wales, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2UW UK
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009 Australia
| | - T. Roose
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering Sciences, Faculty of Engineering and Physical Sciences, University of Southampton, University Road, Southampton, SO17 1BJ UK
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Ramakrishna P, Barberon M. Polarized transport across root epithelia. CURRENT OPINION IN PLANT BIOLOGY 2019; 52:23-29. [PMID: 31323542 DOI: 10.1016/j.pbi.2019.05.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/22/2019] [Accepted: 05/23/2019] [Indexed: 06/10/2023]
Abstract
Plant roots explore the soil to acquire water and nutrients which are often available at concentrations that drastically differ from the plant's actual need for growth and development. This stark difference between availability and requirement can be dealt with owing to the root's architecture as an inverted gut. In roots, the two epithelial characteristics (selective acquisition and diffusion barrier) are split between two cell layers: the epidermis at the root periphery and the endodermis as the innermost cortical cell layer around the vasculature. Polarized transport of nutrients across the root epithelium can be achieved through different pathways: apoplastic, symplastic, or coupled transcellular. This review highlights different features of the root that allow this polarized transport. Special emphasis is placed on the coupled transcellular pathway, facilitated by polarized nutrient carriers along root cell layers but barred by suberin lamellae in endodermal cells.
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Affiliation(s)
- Priya Ramakrishna
- Department of Botany and Plant Biology, University of Geneva, 30 Quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Marie Barberon
- Department of Botany and Plant Biology, University of Geneva, 30 Quai Ernest Ansermet, 1211 Geneva, Switzerland.
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29
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Kirk GJ, Boghi A, Affholder M, Keyes SD, Heppell J, Roose T. Soil carbon dioxide venting through rice roots. PLANT, CELL & ENVIRONMENT 2019; 42:3197-3207. [PMID: 31378945 PMCID: PMC6972674 DOI: 10.1111/pce.13638] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/29/2019] [Accepted: 07/31/2019] [Indexed: 05/12/2023]
Abstract
The growth of rice in submerged soils depends on its ability to form continuous gas channels-aerenchyma-through which oxygen (O2 ) diffuses from the shoots to aerate the roots. Less well understood is the extent to which aerenchyma permits venting of respiratory carbon dioxide (CO2 ) in the opposite direction. Large, potentially toxic concentrations of dissolved CO2 develop in submerged rice soils. We show using X-ray computed tomography and image-based mathematical modelling that CO2 venting through rice roots is far greater than thought hitherto. We found rates of venting equivalent to a third of the daily CO2 fixation in photosynthesis. Without this venting through the roots, the concentrations of CO2 and associated bicarbonate (HCO3- ) in root cells would have been well above levels known to be toxic to roots. Removal of CO2 and hence carbonic acid (H2 CO3 ) from the soil was sufficient to increase the pH in the rhizosphere close to the roots by 0.7 units, which is sufficient to solubilize or immobilize various nutrients and toxicants. A sensitivity analysis of the model showed that such changes are expected for a wide range of plant and soil conditions.
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Affiliation(s)
- Guy J.D. Kirk
- School of Water, Energy and EnvironmentCranfield UniversityCranfieldUK
| | - Andrea Boghi
- School of Water, Energy and EnvironmentCranfield UniversityCranfieldUK
- Faculty of Engineering and EnvironmentUniversity of SouthamptonSouthamptonUK
| | | | - Samuel D. Keyes
- Faculty of Engineering and EnvironmentUniversity of SouthamptonSouthamptonUK
| | - James Heppell
- Faculty of Engineering and EnvironmentUniversity of SouthamptonSouthamptonUK
| | - Tiina Roose
- Faculty of Engineering and EnvironmentUniversity of SouthamptonSouthamptonUK
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Approximate nutrient flux and concentration solutions of the Nye-Tinker-Barber model by the perturbation expansion method. J Theor Biol 2019; 476:19-29. [PMID: 31128141 DOI: 10.1016/j.jtbi.2019.05.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 05/19/2019] [Accepted: 05/22/2019] [Indexed: 11/23/2022]
Abstract
The Nye-Tinker-Barber model is a basic and representative one for single-ion nutrient uptake by plant root from the soil and we aim to derive its approximate analytical solutions of flux and concentration. We divide the rhizosphere into the inner and the outer fields, match the inner and the outer solutions near the root surface, and then obtain the approximate analytical solutions of nutrient uptake flux at the root surface and global nutrient concentration of the diffusion or the convection-diffusion Nye-Tinker-Barber model. The analytical and numerical fluxes of K+ and [Formula: see text] decay quickly to 0 in less than 3 days while [Formula: see text] and Cd2+ gradually decrease in more than 15 days; the depletion profile spread of [Formula: see text] is apparently narrower than [Formula: see text] and K+ in 24 days. The different flux and concentration patterns of 4 nutrients result from their mobility and solubility in the rhizosphere. In comparison with the numerical simulations and the previous analytical results, we find that the analytical flux will overestimate the numerical flux of [Formula: see text] and Cd2+ while the analytical concentration can accurately predict the numerical concentration; the flux and the concentration solutions of the convection-diffusion Nye-Tinker-Barber model can be simplified to the diffusion versions by the Péclet number, and they can more widely describe the transport of nutrients of different attributes in soils of different textures with different levels of saturation, conductivity and permeability.
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Passot S, Couvreur V, Meunier F, Draye X, Javaux M, Leitner D, Pagès L, Schnepf A, Vanderborght J, Lobet G. Connecting the dots between computational tools to analyse soil-root water relations. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2345-2357. [PMID: 30329081 DOI: 10.1093/jxb/ery361] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 10/10/2018] [Indexed: 05/20/2023]
Abstract
In recent years, many computational tools, such as image analysis, data management, process-based simulation, and upscaling tools, have been developed to help quantify and understand water flow in the soil-root system, at multiple scales (tissue, organ, plant, and population). Several of these tools work together or at least are compatible. However, for the uninformed researcher, they might seem disconnected, forming an unclear and disorganized succession of tools. In this article, we show how different studies can be further developed by connecting them to analyse soil-root water relations in a comprehensive and structured network. This 'explicit network of soil-root computational tools' informs readers about existing tools and helps them understand how their data (past and future) might fit within the network. We also demonstrate the novel possibilities of scale-consistent parameterizations made possible by the network with a set of case studies from the literature. Finally, we discuss existing gaps in the network and how we can move forward to fill them.
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Affiliation(s)
- Sixtine Passot
- Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Valentin Couvreur
- Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Félicien Meunier
- Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
- Computational and Applied Vegetation Ecology lab, Ghent University, Gent, Belgium
- Department of Earth and Environment, Boston University, Boston, MA, USA
| | - Xavier Draye
- Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Mathieu Javaux
- Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
- Agrosphere, IBG3, Forschungszentrum Jülich, GmbH Jülich, Germany
| | | | | | - Andrea Schnepf
- Agrosphere, IBG3, Forschungszentrum Jülich, GmbH Jülich, Germany
| | - Jan Vanderborght
- Agrosphere, IBG3, Forschungszentrum Jülich, GmbH Jülich, Germany
| | - Guillaume Lobet
- Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
- Agrosphere, IBG3, Forschungszentrum Jülich, GmbH Jülich, Germany
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Koebernick N, Daly KR, Keyes SD, Bengough AG, Brown LK, Cooper LJ, George TS, Hallett PD, Naveed M, Raffan A, Roose T. Imaging microstructure of the barley rhizosphere: particle packing and root hair influences. THE NEW PHYTOLOGIST 2019; 221:1878-1889. [PMID: 30289555 DOI: 10.1111/nph.15516] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/23/2018] [Indexed: 05/10/2023]
Abstract
Soil adjacent to roots has distinct structural and physical properties from bulk soil, affecting water and solute acquisition by plants. Detailed knowledge on how root activity and traits such as root hairs affect the three-dimensional pore structure at a fine scale is scarce and often contradictory. Roots of hairless barley (Hordeum vulgare L. cv Optic) mutant (NRH) and its wildtype (WT) parent were grown in tubes of sieved (<250 μm) sandy loam soil under two different water regimes. The tubes were scanned by synchrotron-based X-ray computed tomography to visualise pore structure at the soil-root interface. Pore volume fraction and pore size distribution were analysed vs distance within 1 mm of the root surface. Less dense packing of particles at the root surface was hypothesised to cause the observed increased pore volume fraction immediately next to the epidermis. The pore size distribution was narrower due to a decreased fraction of larger pores. There were no statistically significant differences in pore structure between genotypes or moisture conditions. A model is proposed that describes the variation in porosity near roots taking into account soil compaction and the surface effect at the root surface.
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Affiliation(s)
- Nicolai Koebernick
- Bioengineering Sciences Research Group, Engineering Sciences Academic Unit, Faculty of Engineering and the Environment, University of Southampton, Southampton, SO17 1BJ, UK
- Soil Science and Soil Protection, Martin Luther University Halle-Wittenberg, von-Seckendoff-Platz 3, 06120, Halle (Saale), Germany
| | - Keith R Daly
- Bioengineering Sciences Research Group, Engineering Sciences Academic Unit, Faculty of Engineering and the Environment, University of Southampton, Southampton, SO17 1BJ, UK
| | - Samuel D Keyes
- Bioengineering Sciences Research Group, Engineering Sciences Academic Unit, Faculty of Engineering and the Environment, University of Southampton, Southampton, SO17 1BJ, UK
| | - Anthony G Bengough
- Ecological Sciences Group, The James Hutton Institute, Dundee, DD2 5DA, UK
- School of Science and Engineering, University of Dundee, Dundee, DD1 4HN, UK
| | - Lawrie K Brown
- Ecological Sciences Group, The James Hutton Institute, Dundee, DD2 5DA, UK
| | - Laura J Cooper
- Bioengineering Sciences Research Group, Engineering Sciences Academic Unit, Faculty of Engineering and the Environment, University of Southampton, Southampton, SO17 1BJ, UK
- Mathematics Institute, University of Warwick, Warwick, CV4 7AL, UK
| | - Timothy S George
- Ecological Sciences Group, The James Hutton Institute, Dundee, DD2 5DA, UK
| | - Paul D Hallett
- Institute of Biological and Environmental Science, University of Aberdeen, Aberdeen, AB24 3FX, UK
| | - Muhammad Naveed
- Institute of Biological and Environmental Science, University of Aberdeen, Aberdeen, AB24 3FX, UK
- School of Computing and Engineering, University of West London, London, W5 5RF, UK
| | - Annette Raffan
- Institute of Biological and Environmental Science, University of Aberdeen, Aberdeen, AB24 3FX, UK
| | - Tiina Roose
- Bioengineering Sciences Research Group, Engineering Sciences Academic Unit, Faculty of Engineering and the Environment, University of Southampton, Southampton, SO17 1BJ, UK
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Ajmera I, Hodgman TC, Lu C. An Integrative Systems Perspective on Plant Phosphate Research. Genes (Basel) 2019; 10:E139. [PMID: 30781872 PMCID: PMC6410211 DOI: 10.3390/genes10020139] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 01/30/2019] [Accepted: 02/07/2019] [Indexed: 12/31/2022] Open
Abstract
The case for improving crop phosphorus-use-efficiency is widely recognized. Although much is known about the molecular and regulatory mechanisms, improvements have been hampered by the extreme complexity of phosphorus (P) dynamics, which involves soil chemistry; plant-soil interactions; uptake, transport, utilization and remobilization within plants; and agricultural practices. The urgency and direction of phosphate research is also dependent upon the finite sources of P, availability of stocks to farmers and reducing environmental hazards. This work introduces integrative systems approaches as a way to represent and understand this complexity, so that meaningful links can be established between genotype, environment, crop traits and yield. It aims to provide a large set of pointers to potential genes and research practice, with a view to encouraging members of the plant-phosphate research community to adopt such approaches so that, together, we can aid efforts in global food security.
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Affiliation(s)
- Ishan Ajmera
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Loughborough LE12 5RD, UK.
| | - T Charlie Hodgman
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Loughborough LE12 5RD, UK.
| | - Chungui Lu
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Nottingham NG25 0 QF, UK.
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Zhang N, Thompson CEL, Townend IH, Rankin KE, Paterson DM, Manning AJ. Nondestructive 3D Imaging and Quantification of Hydrated Biofilm-Sediment Aggregates Using X-ray Microcomputed Tomography. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:13306-13313. [PMID: 30354082 DOI: 10.1021/acs.est.8b03997] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Biofilm-sediment aggregate (BSA) contains a high water content, either within internal pores and channels or bound by extracellular polymeric substances (EPS) forming a highly hydrated biofilm matrix. Desiccation of BSAs alters the biofilm morphology and thus the physical characteristics of porous media, such as the binding matrix within BSA and internal pore geometry. Observing BSAs in their naturally hydrated form is essential but hampered due to the lack of techniques for imaging and discerning hydrated materials. Generally, imagery techniques (scanning electron microscopy (SEM), transmission electron microscopy (TEM), and focused ion beam nanotomography (FIB-nt)) involve the desiccation of BSAs (freeze-drying or acetone dehydration) or prevent differentiation between BSA components such as inorganic particles and pore water (confocal laser scanning microscopic (CLSM)). Here, we propose a novel methodology that simultaneously achieves the 3D visualization and quantification of BSAs and their components in their hydrated form at a submicron resolution using X-ray microcomputed tomography (μ-CT). It enables the high-resolution detection of comparable morphology of multiphase components within a hydrated aggregate: each single inorganic particle and the hydrated biofilm matrix. This allows the estimation of aggregate density and the illustration of biofilm-sediment binding matrix. This information provides valuable insights into investigations of the transport of BSAs and aggregate-associated sediment particles, contaminants (such as microplastics), organic carbon, and their impacts on aquatic biogeochemical cycling.
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Affiliation(s)
- Naiyu Zhang
- School of Ocean and Earth Science , National Oceanography Centre, University of Southampton , Southampton SO14 3ZH , U.K
| | - Charlotte E L Thompson
- School of Ocean and Earth Science , National Oceanography Centre, University of Southampton , Southampton SO14 3ZH , U.K
| | - Ian H Townend
- School of Ocean and Earth Science , National Oceanography Centre, University of Southampton , Southampton SO14 3ZH , U.K
| | - Kathryn E Rankin
- μ-VIS X-ray Imaging Centre, Faculty of Engineering and the Environment, Highfield Campus , University of Southampton , Southampton SO17 1BJ , U.K
| | - David M Paterson
- Sediment Ecology Research Group, Scottish Oceans Institute, School of Biology , University of St. Andrews , St. Andrews KY16 8LB , U.K
| | - Andrew J Manning
- HR Wallingford Ltd., Coasts & Oceans Group, Wallingford OX10 8BA , United Kingdom
- School of Environmental Sciences , University of Hull , Hull HU6 7RX , United Kingdom
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Keyes SD, Cooper L, Duncan S, Koebernick N, McKay Fletcher DM, Scotson CP, van Veelen A, Sinclair I, Roose T. Measurement of micro-scale soil deformation around roots using four-dimensional synchrotron tomography and image correlation. J R Soc Interface 2018; 14:rsif.2017.0560. [PMID: 29118113 DOI: 10.1098/rsif.2017.0560] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/13/2017] [Indexed: 01/19/2023] Open
Abstract
This study applied time lapse (four-dimensional) synchrotron X-ray computed tomography to observe micro-scale interactions between plant roots and soil. Functionally contrasting maize root tips were repeatedly imaged during ingress into soil columns of varying water content and compaction. This yielded sequences of three-dimensional densiometric data, representing time-resolved geometric soil and root configurations at the micronmetre scale. These data were used as inputs for two full-field kinematic quantification methods, which enabled the analysis of three-dimensional soil deformation around elongating roots. Discrete object tracking was used to track rigid mineral grains, while continuum digital volume correlation was used to track grey-level patterns within local sub-volumes. These techniques both allowed full-field soil displacements to be quantified at an intra-rhizosphere spatial sampling scale of less than 300 µm. Significant differences in deformation mechanisms were identified around different phenotypes under different soil conditions. A uniquely strong contrast was observed between intact and de-capped roots grown in dry, compacted soil. This provides evidence that functional traits of the root cap significantly reduce the amount of soil disturbance per unit of root elongation, with this effect being particularly significant in drier soil.
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Affiliation(s)
- S D Keyes
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, Faculty of Engineering and Environment, University of Southampton, University Road, Southampton SO17 1BJ, UK
| | - L Cooper
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, Faculty of Engineering and Environment, University of Southampton, University Road, Southampton SO17 1BJ, UK
| | - S Duncan
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, Faculty of Engineering and Environment, University of Southampton, University Road, Southampton SO17 1BJ, UK
| | - N Koebernick
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, Faculty of Engineering and Environment, University of Southampton, University Road, Southampton SO17 1BJ, UK
| | - D M McKay Fletcher
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, Faculty of Engineering and Environment, University of Southampton, University Road, Southampton SO17 1BJ, UK
| | - C P Scotson
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, Faculty of Engineering and Environment, University of Southampton, University Road, Southampton SO17 1BJ, UK
| | - A van Veelen
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, Faculty of Engineering and Environment, University of Southampton, University Road, Southampton SO17 1BJ, UK
| | - I Sinclair
- Materials Engineering Group, Department of Mechanical Engineering, Faculty of Engineering and Environment, University of Southampton, University Road, Southampton SO17 1BJ, UK
| | - T Roose
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, Faculty of Engineering and Environment, University of Southampton, University Road, Southampton SO17 1BJ, UK
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Rabbi SMF, Tighe MK, Flavel RJ, Kaiser BN, Guppy CN, Zhang X, Young IM. Plant roots redesign the rhizosphere to alter the three-dimensional physical architecture and water dynamics. THE NEW PHYTOLOGIST 2018; 219:542-550. [PMID: 29774952 DOI: 10.1111/nph.15213] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/01/2018] [Indexed: 05/13/2023]
Abstract
The mechanisms controlling the genesis of rhizosheaths are not well understood, despite their importance in controlling the flux of nutrients and water from soil to root. Here, we examine the development of rhizosheaths from drought-tolerant and drought-sensitive chickpea varieties; focusing on the three-dimensional characterization of the pore volume (> 16 μm voxel spatial resolution) obtained from X-ray microtomography, along with the characterization of mucilage and root hairs, and water sorption. We observe that drought-tolerant plants generate a larger diameter root, and a greater and more porous mass of rhizosheath, which also has a significantly increased water sorptivity, as compared with bulk soil. Using lattice Boltzmann simulations of soil permeability, we find that the root activity of both cultivars creates an anisotropic structure in the rhizosphere, in that its ability to conduct water in the radial direction is significantly higher than in the axial direction, especially in the drought-tolerant cultivar. We suggest that significant differences in rhizosheath architectures are sourced not only by changes in structure of the volumes, but also from root mucilage, and further suggest that breeding for rhizosheath architectures and function may be a potential future avenue for better designing crops in a changing environment.
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Affiliation(s)
- Sheikh M F Rabbi
- School of Life and Environmental Sciences, ARC Industrial Transformation Research Hub - Legumes for Sustainable Agriculture, University of Sydney, Camperdown, Sydney, NSW, 2006, Australia
| | - Matthew K Tighe
- School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - Richard J Flavel
- School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - Brent N Kaiser
- School of Life and Environmental Sciences, ARC Industrial Transformation Research Hub - Legumes for Sustainable Agriculture, University of Sydney, Camperdown, Sydney, NSW, 2006, Australia
| | - Chris N Guppy
- School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - Xiaoxian Zhang
- Rothamsted Research, Sustainable Agriculture Sciences, Harpenden, Hertfordshire, AL 5 2JQ, UK
| | - Iain M Young
- School of Life and Environmental Sciences, ARC Industrial Transformation Research Hub - Legumes for Sustainable Agriculture, University of Sydney, Camperdown, Sydney, NSW, 2006, Australia
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Boghi A, Roose T, Kirk GJD. A Model of Uranium Uptake by Plant Roots Allowing for Root-Induced Changes in the soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:3536-3545. [PMID: 29466669 DOI: 10.1021/acs.est.7b06136] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We develop a model with which to study the poorly understood mechanisms of uranium (U) uptake by plants. The model is based on equations for transport and reaction of U and acids and bases in the rhizosphere around cylindrical plant roots. It allows for the speciation of U with hydroxyl, carbonate, and organic ligands in the soil solution; the nature and kinetics of sorption reactions with the soil solid; and the effects of root-induced changes in rhizosphere pH. A sensitivity analysis showed the importance of soil sorption and speciation parameters as influenced by pH and CO2 pressure; and of root geometry and root-induced acid-base changes linked to the form of nitrogen taken up by the root. The root absorbing coefficient for U, relating influx to the concentration of U species in solution at the root surface, was also important. Simplified empirical models of U uptake by different plant species and soil types need to account for these effects.
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Affiliation(s)
- Andrea Boghi
- School of Water, Energy & Environment , Cranfield University , Cranfield, Bedford MK43 0AL , U.K
| | - Tiina Roose
- Faculty of Engineering and Environment , University of Southampton , Southampton SO17 1BJ , U.K
| | - Guy J D Kirk
- School of Water, Energy & Environment , Cranfield University , Cranfield, Bedford MK43 0AL , U.K
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38
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Mathers AW, Hepworth C, Baillie AL, Sloan J, Jones H, Lundgren M, Fleming AJ, Mooney SJ, Sturrock CJ. Investigating the microstructure of plant leaves in 3D with lab-based X-ray computed tomography. PLANT METHODS 2018; 14:99. [PMID: 30455724 PMCID: PMC6231253 DOI: 10.1186/s13007-018-0367-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/03/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND Leaf cellular architecture plays an important role in setting limits for carbon assimilation and, thus, photosynthetic performance. However, the low density, fine structure, and sensitivity to desiccation of plant tissue has presented challenges to its quantification. Classical methods of tissue fixation and embedding prior to 2D microscopy of sections is both laborious and susceptible to artefacts that can skew the values obtained. Here we report an image analysis pipeline that provides quantitative descriptors of plant leaf intercellular airspace using lab-based X-ray computed tomography (microCT). We demonstrate successful visualisation and quantification of differences in leaf intercellular airspace in 3D for a range of species (including both dicots and monocots) and provide a comparison with a standard 2D analysis of leaf sections. RESULTS We used the microCT image pipeline to obtain estimates of leaf porosity and mesophyll exposed surface area (Smes) for three dicot species (Arabidopsis, tomato and pea) and three monocot grasses (barley, oat and rice). The imaging pipeline consisted of (1) a masking operation to remove the background airspace surrounding the leaf, (2) segmentation by an automated threshold in ImageJ and then (3) quantification of the extracted pores using the ImageJ 'Analyze Particles' tool. Arabidopsis had the highest porosity and lowest Smes for the dicot species whereas barley had the highest porosity and the highest Smes for the grass species. Comparison of porosity and Smes estimates from 3D microCT analysis and 2D analysis of sections indicates that both methods provide a comparable estimate of porosity but the 2D method may underestimate Smes by almost 50%. A deeper study of porosity revealed similarities and differences in the asymmetric distribution of airspace between the species analysed. CONCLUSIONS Our results demonstrate the utility of high resolution imaging of leaf intercellular airspace networks by lab-based microCT and provide quantitative data on descriptors of leaf cellular architecture. They indicate there is a range of porosity and Smes values in different species and that there is not a simple relationship between these parameters, suggesting the importance of cell size, shape and packing in the determination of cellular parameters proposed to influence leaf photosynthetic performance.
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Affiliation(s)
- Andrew W. Mathers
- Division of Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD UK
| | - Christopher Hepworth
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN UK
| | - Alice L. Baillie
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN UK
| | - Jen Sloan
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN UK
| | - Hannah Jones
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN UK
| | - Marjorie Lundgren
- Lancaster Environment Centre, Lancaster University, LEC 2 Yellow Zone B43, Lancaster, LA1 4YQ UK
| | - Andrew J. Fleming
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN UK
| | - Sacha J. Mooney
- Division of Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD UK
| | - Craig J. Sturrock
- Division of Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD UK
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Carminati A, Passioura JB, Zarebanadkouki M, Ahmed MA, Ryan PR, Watt M, Delhaize E. Root hairs enable high transpiration rates in drying soils. THE NEW PHYTOLOGIST 2017; 216:771-781. [PMID: 28758687 DOI: 10.1111/nph.14715] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 06/21/2017] [Indexed: 05/24/2023]
Abstract
Do root hairs help roots take up water from the soil? Despite the well-documented role of root hairs in phosphate uptake, their role in water extraction is controversial. We grew barley (Hordeum vulgare cv Pallas) and its root-hairless mutant brb in a root pressure chamber, whereby the transpiration rate could be varied whilst monitoring the suction in the xylem. The method provides accurate measurements of the dynamic relationship between the transpiration rate and xylem suction. The relationship between the transpiration rate and xylem suction was linear in wet soils and did not differ between genotypes. When the soil dried, the xylem suction increased rapidly and non-linearly at high transpiration rates. This response was much greater with the brb mutant, implying a reduced capacity to take up water. We conclude that root hairs facilitate the uptake of water by substantially reducing the drop in matric potential at the interface between root and soil in rapidly transpiring plants. The experiments also reinforce earlier observations that there is a marked hysteresis in the suction in the xylem when the transpiration rate is rising compared with when it is falling, and possible reasons for this behavior are discussed.
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Affiliation(s)
- Andrea Carminati
- Chair of Soil Physics, University of Bayreuth, Bauyreuth, D-95447, Germany
| | - John B Passioura
- CSIRO Agriculture and Food, GPO Box 1600, Canberra, ACT, 2601, Australia
| | | | - Mutez A Ahmed
- Chair of Soil Physics, University of Bayreuth, Bauyreuth, D-95447, Germany
- Division of Soil Hydrology, Georg-August Universität, D-37073, Göttingen, Germany
- Department of Agricultural Engineering, Faculty of Agriculture, University of Khartoum, Khartoum North, 13314, Shambat, Sudan
| | - Peter R Ryan
- CSIRO Agriculture and Food, GPO Box 1600, Canberra, ACT, 2601, Australia
| | - Michelle Watt
- Plant Sciences, Institute of Bio- and Geosciences, Jülich Forschungszentrum, Jülich, D-52425, Germany
| | - Emmanuel Delhaize
- CSIRO Agriculture and Food, GPO Box 1600, Canberra, ACT, 2601, Australia
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Helliwell JR, Sturrock CJ, Mairhofer S, Craigon J, Ashton RW, Miller AJ, Whalley WR, Mooney SJ. The emergent rhizosphere: imaging the development of the porous architecture at the root-soil interface. Sci Rep 2017; 7:14875. [PMID: 29093533 PMCID: PMC5665926 DOI: 10.1038/s41598-017-14904-w] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 10/17/2017] [Indexed: 11/10/2022] Open
Abstract
The rhizosphere is the zone of soil influenced by a plant root and is critical for plant health and nutrient acquisition. All below ground resources must pass through this dynamic zone prior to their capture by plant roots. However, researching the undisturbed rhizosphere has proved very challenging. Here we compare the temporal changes to the intact rhizosphere pore structure during the emergence of a developing root system in different soils. High resolution X-ray Computed Tomography (CT) was used to quantify the impact of root development on soil structural change, at scales relevant to individual micro-pores and aggregates (µm). A comparison of micro-scale structural evolution in homogenously packed soils highlighted the impacts of a penetrating root system in changing the surrounding porous architecture and morphology. Results indicate the structural zone of influence of a root can be more localised than previously reported (µm scale rather than mm scale). With time, growing roots significantly alter the soil physical environment in their immediate vicinity through reducing root-soil contact and crucially increasing porosity at the root-soil interface and not the converse as has often been postulated. This 'rhizosphere pore structure' and its impact on associated dynamics are discussed.
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Affiliation(s)
- J R Helliwell
- Division of Agricultural and Environmental Sciences, Gateway Building, Sutton Bonington Campus, University of Nottingham, Leicestershire, LE12 5RD, UK
- Sustainable Soils and Grassland Systems Department, Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - C J Sturrock
- Division of Agricultural and Environmental Sciences, Gateway Building, Sutton Bonington Campus, University of Nottingham, Leicestershire, LE12 5RD, UK
| | - S Mairhofer
- Division of Agricultural and Environmental Sciences, Gateway Building, Sutton Bonington Campus, University of Nottingham, Leicestershire, LE12 5RD, UK
| | - J Craigon
- Division of Agricultural and Environmental Sciences, Gateway Building, Sutton Bonington Campus, University of Nottingham, Leicestershire, LE12 5RD, UK
| | - R W Ashton
- Sustainable Soils and Grassland Systems Department, Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - A J Miller
- Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - W R Whalley
- Sustainable Soils and Grassland Systems Department, Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - S J Mooney
- Division of Agricultural and Environmental Sciences, Gateway Building, Sutton Bonington Campus, University of Nottingham, Leicestershire, LE12 5RD, UK.
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Zeller-Plumhoff B, Roose T, Clough GF, Schneider P. Image-based modelling of skeletal muscle oxygenation. J R Soc Interface 2017; 14:rsif.2016.0992. [PMID: 28202595 DOI: 10.1098/rsif.2016.0992] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/25/2017] [Indexed: 12/12/2022] Open
Abstract
The supply of oxygen in sufficient quantity is vital for the correct functioning of all organs in the human body, in particular for skeletal muscle during exercise. Disease is often associated with both an inhibition of the microvascular supply capability and is thought to relate to changes in the structure of blood vessel networks. Different methods exist to investigate the influence of the microvascular structure on tissue oxygenation, varying over a range of application areas, i.e. biological in vivo and in vitro experiments, imaging and mathematical modelling. Ideally, all of these methods should be combined within the same framework in order to fully understand the processes involved. This review discusses the mathematical models of skeletal muscle oxygenation currently available that are based upon images taken of the muscle microvasculature in vivo and ex vivo Imaging systems suitable for capturing the blood vessel networks are discussed and respective contrasting methods presented. The review further informs the association between anatomical characteristics in health and disease. With this review we give the reader a tool to understand and establish the workflow of developing an image-based model of skeletal muscle oxygenation. Finally, we give an outlook for improvements needed for measurements and imaging techniques to adequately investigate the microvascular capability for oxygen exchange.
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Affiliation(s)
- B Zeller-Plumhoff
- Helmholtz-Zentrum für Material- und Küstenforschung, Geesthacht, Germany .,Bioengineering Research Group, Faculty of Engineering and the Environment, University of Southampton, Southampton, UK
| | - T Roose
- Bioengineering Research Group, Faculty of Engineering and the Environment, University of Southampton, Southampton, UK
| | - G F Clough
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - P Schneider
- Bioengineering Research Group, Faculty of Engineering and the Environment, University of Southampton, Southampton, UK
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Keyes SD, Zygalakis KC, Roose T. An Explicit Structural Model of Root Hair and Soil Interactions Parameterised by Synchrotron X-ray Computed Tomography. Bull Math Biol 2017; 79:2785-2813. [PMID: 29030805 PMCID: PMC5709508 DOI: 10.1007/s11538-017-0350-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 09/19/2017] [Indexed: 11/29/2022]
Abstract
The rhizosphere is a zone of fundamental importance for understanding the dynamics of nutrient acquisition by plant roots. The canonical difficulty of experimentally investigating the rhizosphere led long ago to the adoption of mathematical models, the most sophisticated of which now incorporate explicit representations of root hairs and rhizosphere soil. Mathematical upscaling regimes, such as homogenisation, offer the possibility of incorporating into larger-scale models the important mechanistic processes occurring at the rhizosphere scale. However, we lack concrete descriptions of all the features required to fully parameterise models at the rhizosphere scale. By combining synchrotron X-ray computed tomography (SRXCT) and a novel root growth assay, we derive a three-dimensional description of rhizosphere soil structure suitable for use in multi-scale modelling frameworks. We describe an approach to mitigate sub-optimal root hair detection via structural root hair growth modelling. The growth model is explicitly parameterised with SRXCT data and simulates three-dimensional root hair ideotypes in silico, which are suitable for both ideotypic analysis and parameterisation of 3D geometry in mathematical models. The study considers different hypothetical conditions governing root hair interactions with soil matrices, with their respective effects on hair morphology being compared between idealised and image-derived soil/root geometries. The studies in idealised geometries suggest that packing arrangement of soil affects hair tortuosity more than the particle diameter. Results in field-derived soil suggest that hair access to poorly mobile nutrients is particularly sensitive to the physical interaction between the growing hairs and the phase of the soil in which soil water is present (i.e. the hydrated textural phase). The general trends in fluid-coincident hair length with distance from the root, and their dependence on hair/soil interaction mechanisms, are conserved across Cartesian and cylindrical geometries.
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Affiliation(s)
- Samuel David Keyes
- Bioengineering Sciences Research Group, Faculty of Engineering and Environment, University of Southampton, Southampton, SO17 1BJ, UK.
| | | | - Tiina Roose
- Bioengineering Sciences Research Group, Faculty of Engineering and Environment, University of Southampton, Southampton, SO17 1BJ, UK
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Koebernick N, Daly KR, Keyes SD, George TS, Brown LK, Raffan A, Cooper LJ, Naveed M, Bengough AG, Sinclair I, Hallett PD, Roose T. High-resolution synchrotron imaging shows that root hairs influence rhizosphere soil structure formation. THE NEW PHYTOLOGIST 2017; 216:124-135. [PMID: 28758681 PMCID: PMC5601222 DOI: 10.1111/nph.14705] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/12/2017] [Indexed: 05/17/2023]
Abstract
In this paper, we provide direct evidence of the importance of root hairs on pore structure development at the root-soil interface during the early stage of crop establishment. This was achieved by use of high-resolution (c. 5 μm) synchrotron radiation computed tomography (SRCT) to visualise both the structure of root hairs and the soil pore structure in plant-soil microcosms. Two contrasting genotypes of barley (Hordeum vulgare), with and without root hairs, were grown for 8 d in microcosms packed with sandy loam soil at 1.2 g cm-3 dry bulk density. Root hairs were visualised within air-filled pore spaces, but not in the fine-textured soil regions. We found that the genotype with root hairs significantly altered the porosity and connectivity of the detectable pore space (> 5 μm) in the rhizosphere, as compared with the no-hair mutants. Both genotypes showed decreasing pore space between 0.8 and 0.1 mm from the root surface. Interestingly the root-hair-bearing genotype had a significantly greater soil pore volume-fraction at the root-soil interface. Effects of pore structure on diffusion and permeability were estimated to be functionally insignificant under saturated conditions when simulated using image-based modelling.
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Affiliation(s)
- Nicolai Koebernick
- Bioengineering Sciences Research GroupEngineering Sciences Academic UnitFaculty of Engineering and the EnvironmentUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Keith R. Daly
- Bioengineering Sciences Research GroupEngineering Sciences Academic UnitFaculty of Engineering and the EnvironmentUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Samuel D. Keyes
- Bioengineering Sciences Research GroupEngineering Sciences Academic UnitFaculty of Engineering and the EnvironmentUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Timothy S. George
- Ecological Sciences GroupThe James Hutton InstituteInvergowrieDundeeDD2 5DAUK
| | - Lawrie K. Brown
- Ecological Sciences GroupThe James Hutton InstituteInvergowrieDundeeDD2 5DAUK
| | - Annette Raffan
- Institute of Biological and Environmental ScienceUniversity of AberdeenAberdeenAB24 3UUUK
| | - Laura J. Cooper
- Bioengineering Sciences Research GroupEngineering Sciences Academic UnitFaculty of Engineering and the EnvironmentUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Muhammad Naveed
- Institute of Biological and Environmental ScienceUniversity of AberdeenAberdeenAB24 3UUUK
| | - Anthony G. Bengough
- Ecological Sciences GroupThe James Hutton InstituteInvergowrieDundeeDD2 5DAUK
- School of Science and EngineeringUniversity of DundeeDundeeDD1 4HNUK
| | - Ian Sinclair
- Bioengineering Sciences Research GroupEngineering Sciences Academic UnitFaculty of Engineering and the EnvironmentUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Paul D. Hallett
- Institute of Biological and Environmental ScienceUniversity of AberdeenAberdeenAB24 3UUUK
| | - Tiina Roose
- Bioengineering Sciences Research GroupEngineering Sciences Academic UnitFaculty of Engineering and the EnvironmentUniversity of SouthamptonSouthamptonSO17 1BJUK
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Ramakrishnan M, Ceasar SA, Vinod KK, Duraipandiyan V, Ajeesh Krishna TP, Upadhyaya HD, Al-Dhabi NA, Ignacimuthu S. Identification of putative QTLs for seedling stage phosphorus starvation response in finger millet (Eleusine coracana L. Gaertn.) by association mapping and cross species synteny analysis. PLoS One 2017; 12:e0183261. [PMID: 28820887 PMCID: PMC5562303 DOI: 10.1371/journal.pone.0183261] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 08/01/2017] [Indexed: 01/02/2023] Open
Abstract
A germplasm assembly of 128 finger millet genotypes from 18 countries was evaluated for seedling-stage phosphorus (P) responses by growing them in P sufficient (Psuf) and P deficient (Pdef) treatments. Majority of the genotypes showed adaptive responses to low P condition. Based on phenotype behaviour using the best linear unbiased predictors for each trait, genotypes were classified into, P responsive, low P tolerant and P non-responsive types. Based on the overall phenotype performance under Pdef, 10 genotypes were identified as low P tolerants. The low P tolerant genotypes were characterised by increased shoot and root length and increased root hair induction with longer root hairs under Pdef, than under Psuf. Association mapping of P response traits using mixed linear models revealed four quantitative trait loci (QTLs). Two QTLs (qLRDW.1 and qLRDW.2) for low P response affecting root dry weight explained over 10% phenotypic variation. In silico synteny analysis across grass genomes for these QTLs identified putative candidate genes such as Ser-Thr kinase and transcription factors such as WRKY and basic helix-loop-helix (bHLH). The QTLs for response under Psuf were mapped for traits such as shoot dry weight (qHSDW.1) and root length (qHRL.1). Putative associations of these QTLs over the syntenous regions on the grass genomes revealed proximity to cytochrome P450, phosphate transporter and pectin methylesterase inhibitor (PMEI) genes. This is the first report of the extent of phenotypic variability for P response in finger millet genotypes during seedling-stage, along with the QTLs and putative candidate genes associated with P starvation tolerance.
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Affiliation(s)
- M. Ramakrishnan
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, India
| | - S. Antony Ceasar
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, India
- Centre for Plant Sciences and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - K. K. Vinod
- ICAR-Indian Agricultural Research Institute, Rice Breeding and Genetics Research Centre, Aduthurai, Tamil Nadu, India
| | - V. Duraipandiyan
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, India
- Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - T. P. Ajeesh Krishna
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, India
| | - Hari D. Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
| | - N. A. Al-Dhabi
- Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - S. Ignacimuthu
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, India
- The International Scientific Partnership Program (ISPP), King Saud University, Vice-19 Rectorate for Graduate studies and Research, Riyadh, Kingdom of Saudi Arabia
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Keyes SD, Gostling NJ, Cheung JH, Roose T, Sinclair I, Marchant A. The Application of Contrast Media for In Vivo Feature Enhancement in X-Ray Computed Tomography of Soil-Grown Plant Roots. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2017; 23:538-552. [PMID: 28320487 DOI: 10.1017/s1431927617000319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The use of in vivo X-ray microcomputed tomography (μCT) to study plant root systems has become routine, but is often hampered by poor contrast between roots, soil, soil water, and soil organic matter. In clinical radiology, imaging of poorly contrasting regions is frequently aided by the use of radio-opaque contrast media. In this study, we present evidence for the utility of iodinated contrast media (ICM) in the study of plant root systems using μCT. Different dilutions of an ionic and nonionic ICM (Gastrografin 370 and Niopam 300) were perfused into the aerial vasculature of juvenile pea plants via a leaf flap (Pisum sativum). The root systems were imaged via μCT, and a variety of image-processing approaches used to quantify and compare the magnitude of the contrast enhancement between different regions. Though the treatment did not appear to significantly aid extraction of full root system architectures from the surrounding soil, it did allow the xylem and phloem units of seminal roots and the vascular morphology within rhizobial nodules to be clearly visualized. The nonionic, low-osmolality contrast agent Niopam appeared to be well tolerated by the plant, whereas Gastrografin showed evidence of toxicity. In summary, the use of iodine-based contrast media allows usually poorly contrasting root structures to be visualized nondestructively using X-ray μCT. In particular, the vascular structures of roots and rhizobial nodules can be clearly visualized in situ.
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Affiliation(s)
- Samuel D Keyes
- 2The Faculty of Engineering and the Environment,The University of Southampton,Southampton,SO17 1BJ,UK
| | - Neil J Gostling
- 1The Centre for Biological Sciences,The University of Southampton,Southampton,SO17 1BJ,UK
| | - Jessica H Cheung
- 1The Centre for Biological Sciences,The University of Southampton,Southampton,SO17 1BJ,UK
| | - Tiina Roose
- 2The Faculty of Engineering and the Environment,The University of Southampton,Southampton,SO17 1BJ,UK
| | - Ian Sinclair
- 2The Faculty of Engineering and the Environment,The University of Southampton,Southampton,SO17 1BJ,UK
| | - Alan Marchant
- 1The Centre for Biological Sciences,The University of Southampton,Southampton,SO17 1BJ,UK
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Schmidt JE, Gaudin ACM. Toward an Integrated Root Ideotype for Irrigated Systems. TRENDS IN PLANT SCIENCE 2017; 22:433-443. [PMID: 28262426 DOI: 10.1016/j.tplants.2017.02.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 01/23/2017] [Accepted: 02/06/2017] [Indexed: 05/24/2023]
Abstract
Breeding towards root-centric ideotypes can be a relatively quick trait-based strategy to improve crop resource use efficiency. Irrigated agriculture represents a crucial and expanding sector, but its unique parameters require traits distinct from previously proposed rainfed ideotypes. We propose a novel irrigated ideotype that integrates traits across multiple scales to enhance resource use efficiency in irrigated agroecosystems, where resources are concentrated in a relatively shallow 'critical zone'. Unique components of this ideotype include rapid transplant recovery and establishment, enhanced exploitation of localized resource hotspots, adaptive physiological regulation, maintenance of hydraulic conductivity, beneficial rhizosphere interactions, and salinity/waterlogging avoidance. If augmented by future research, this target could help to enhance agricultural sustainability in irrigated agroecosystems by guiding the creation of resource-efficient cultivars.
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Affiliation(s)
- Jennifer E Schmidt
- Department of Plant Sciences, University of California (UC) Davis, Davis, CA 95616, USA
| | - Amélie C M Gaudin
- Department of Plant Sciences, University of California (UC) Davis, Davis, CA 95616, USA.
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Horn R, Wingen LU, Snape JW, Dolan L. Mapping of quantitative trait loci for root hair length in wheat identifies loci that co-locate with loci for yield components. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4535-43. [PMID: 27315832 PMCID: PMC4973729 DOI: 10.1093/jxb/erw228] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Root hairs are fast growing, ephemeral tubular extensions of the root epidermis. They arise in the unsuberized maturation zone of the root, effectively increasing the root surface area in the region over which nutrient and water uptake occur. Variation in root hair length (RHL) between varieties has been shown to be genetically determined, and could, therefore, have consequences for nutrient capture and yield potential in crops. We describe the development of a medium-to-high throughput screening method for assessing RHL in wheat at the seedling stage. This method was used to screen a number of wheat mapping population parental lines for variation in RHL. Parents of two populations derived from inter-varietal crosses differed for RHL: Spark vs Rialto and Charger vs Badger. We identified quantitative trait loci (QTLs) for RHL in the populations derived from these crosses. In Spark × Rialto, QTLs on chromosomes 1A, 2A and 6A were associated with variation in RHL, whilst in Charger × Badger, a QTL for RHL was identified on 2BL. The QTLs on 2A and 6A co-localized with previously described QTLs for yield components. Longer root hairs may confer an advantage by exploiting limiting mineral and water resources. This first QTL analysis of root hair length in wheat identifies loci that could usefully be further investigated for their role in tolerance to limiting conditions.
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Affiliation(s)
- R Horn
- Department of Crop Genetics, The John Innes Centre, Norwich NR4 7UH, UK
| | - L U Wingen
- Department of Crop Genetics, The John Innes Centre, Norwich NR4 7UH, UK
| | - J W Snape
- Department of Crop Genetics, The John Innes Centre, Norwich NR4 7UH, UK
| | - L Dolan
- Department of Crop Genetics, The John Innes Centre, Norwich NR4 7UH, UK Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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48
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Nestler J, Keyes SD, Wissuwa M. Root hair formation in rice (Oryza sativa L.) differs between root types and is altered in artificial growth conditions. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3699-708. [PMID: 26976815 DOI: 10.1093/jxb/erw115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Root hairs are important sites for nutrient uptake, especially in P limiting conditions. Here we provide first insights into root hair development for the diverse root types of rice grown under different conditions, and show the first in situ images of rice root hairs in intact soil. Roots of plants grown in upland fields produced short root hairs that showed little responsiveness to P deficiency, and had a higher root hair density in the high P condition. These results were reproducible in rhizoboxes under greenhouse conditions. Synchrotron-based in situ analysis of root hairs in intact soil further confirmed this pattern of root hair formation. In contrast, plants grown in nutrient solution produced more and longer root hairs in low P conditions, but these were unequally distributed among the different root types. While nutrient solution-grown main roots had longer hairs compared to upland field-grown main roots, second order lateral roots did not form any root hairs in nutrient solution-grown plants. Furthermore, root hair formation for plants grown in flooded lowland fields revealed few similarities with those grown in nutrient solution, thus defining nutrient solution as a possible measure of maximal, but not natural root hair development. By combining root hair length and density as a measure for root hair impact on the whole soil-grown root system we show that lateral roots provided the majority of root hair surface.
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Affiliation(s)
- Josefine Nestler
- Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Samuel David Keyes
- Faculty of Engineering and Environment, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Matthias Wissuwa
- Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
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49
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York LM, Carminati A, Mooney SJ, Ritz K, Bennett MJ. The holistic rhizosphere: integrating zones, processes, and semantics in the soil influenced by roots. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3629-43. [PMID: 26980751 DOI: 10.1093/jxb/erw108] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Despite often being conceptualized as a thin layer of soil around roots, the rhizosphere is actually a dynamic system of interacting processes. Hiltner originally defined the rhizosphere as the soil influenced by plant roots. However, soil physicists, chemists, microbiologists, and plant physiologists have studied the rhizosphere independently, and therefore conceptualized the rhizosphere in different ways and using contrasting terminology. Rather than research-specific conceptions of the rhizosphere, the authors propose a holistic rhizosphere encapsulating the following components: microbial community gradients, macroorganisms, mucigel, volumes of soil structure modification, and depletion or accumulation zones of nutrients, water, root exudates, volatiles, and gases. These rhizosphere components are the result of dynamic processes and understanding the integration of these processes will be necessary for future contributions to rhizosphere science based upon interdisciplinary collaborations. In this review, current knowledge of the rhizosphere is synthesized using this holistic perspective with a focus on integrating traditionally separated rhizosphere studies. The temporal dynamics of rhizosphere activities will also be considered, from annual fine root turnover to diurnal fluctuations of water and nutrient uptake. The latest empirical and computational methods are discussed in the context of rhizosphere integration. Clarification of rhizosphere semantics, a holistic model of the rhizosphere, examples of integration of rhizosphere studies across disciplines, and review of the latest rhizosphere methods will empower rhizosphere scientists from different disciplines to engage in the interdisciplinary collaborations needed to break new ground in truly understanding the rhizosphere and to apply this knowledge for practical guidance.
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Affiliation(s)
- Larry M York
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK
| | - Andrea Carminati
- Division of Soil Hydrology, Georg-August University of Göttingen, 37077 Göttingen, Germany
| | - Sacha J Mooney
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK
| | - Karl Ritz
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK
| | - Malcolm J Bennett
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK
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50
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Wissuwa M, Kretzschmar T, Rose TJ. From promise to application: root traits for enhanced nutrient capture in rice breeding. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3605-15. [PMID: 27036129 DOI: 10.1093/jxb/erw061] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Improving nutrient uptake is an objective in crop breeding, especially in tropical areas where infertile soils dominate and farmers may not have the resources to improve soil fertility through fertilizer application. Scientific endeavors to understand the genetic basis of nutrient acquisition have mostly followed reverse genetic approaches. This has undoubtedly led to improved understanding of basic principles in root development and nutrient transport. However, little evidence suggests that the genes identified are actively utilized in breeding programs, and the bottleneck has been the failure to establish links between allelic variation for identified genes and performance in the field. Screening experiments typically reveal large genotypic variation in performance under nutrient deficiency, strongly suggesting the presence of superior alleles for genes controlling root growth and/or nutrient uptake processes. Progress in sequencing technology has enabled characterizations of allelic variation across whole genomes and an international effort has recently culminated in the sequencing of 3000 rice genomes from the International Rice Research Institute genebank. Queries of the 3000 rice sequence database offer immediate possibilities to assess the extent to which allelic variation exists for candidate genes. By selecting subsets of accessions, allelic effects can be tested, diagnostic markers developed, and new donors identified. Technological and conceptual advances in phenotyping of root traits offer improved possibilities to assure that trait-allele associations are established in ways that link to field performance. Genotype-to-phenotype relationships can thus be predicted and tested with unprecedented precision, facilitating the discovery and transfer of beneficial nutrition-related alleles and associated markers into existing breeding pipelines.
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Affiliation(s)
- Matthias Wissuwa
- Crop, Livestock and Environment Division, Japan International Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Tobias Kretzschmar
- Genotyping Services Laboratory, International Rice Research Institute, The Philippines
| | - Terry J Rose
- Southern Cross Plant Science, Southern Cross University, Australia
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