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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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Wang G, Jin Z, George TS, Feng G, Zhang L. Arbuscular mycorrhizal fungi enhance plant phosphorus uptake through stimulating hyphosphere soil microbiome functional profiles for phosphorus turnover. THE NEW PHYTOLOGIST 2023; 238:2578-2593. [PMID: 36694293 DOI: 10.1111/nph.18772] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 01/17/2023] [Indexed: 05/19/2023]
Abstract
The extraradical hyphae of arbuscular mycorrhizal (AM) fungi are colonized by different bacteria in natural and agricultural systems, but the mechanisms by which AM fungi interact with the hyphosphere soil microbiome and influence soil organic phosphorus (P) mobilization remain unclear. We grew Medicago in two-compartment microcosms, inoculated with Rhizophagus irregularis, or not, in the root compartment and set up P treatments (without P, with P addition as KH2 PO4 or nonsoluble phytate) in the hyphal compartment. We studied the processes of soil P turnover and characterized the microbiome functional profiles for P turnover in the hyphosphere soil by metagenomic sequencing. Compared with the bulk soil, the hyphosphere soil of R. irregularis was inhabited by a specific bacterial community and their functional profiles for P turnover was stimulated. At the species level, the shift in hyphosphere soil microbiome was characterized by the recruitment of the genome bin2.39 harbouring both gcd and phoD genes and genome bin2.97 harbouring the phoD gene, which synergistically drove nonsoluble phytate mobilization in the hyphosphere soil. Our results suggest that AM fungi recruits a specific hyphosphere soil microbiome and stimulated their functional profiles for P turnover to enhance utilization of phytate.
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Affiliation(s)
- Guiwei Wang
- College of Resources and Environmental Sciences, MOE Key Laboratory of Plant-Soil Interactions, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | - Zexing Jin
- College of Resources and Environmental Sciences, MOE Key Laboratory of Plant-Soil Interactions, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | | | - Gu Feng
- College of Resources and Environmental Sciences, MOE Key Laboratory of Plant-Soil Interactions, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | - Lin Zhang
- College of Resources and Environmental Sciences, MOE Key Laboratory of Plant-Soil Interactions, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
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Czymmek KJ, Duncan KE, Berg H. Realizing the Full Potential of Advanced Microscopy Approaches for Interrogating Plant-Microbe Interactions. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:245-255. [PMID: 36947723 DOI: 10.1094/mpmi-10-22-0208-fi] [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: 06/18/2023]
Abstract
Microscopy has served as a fundamental tool for insight and discovery in plant-microbe interactions for centuries. From classical light and electron microscopy to corresponding specialized methods for sample preparation and cellular contrasting agents, these approaches have become routine components in the toolkit of plant and microbiology scientists alike to visualize, probe and understand the nature of host-microbe relationships. Over the last three decades, three-dimensional perspectives led by the development of electron tomography, and especially, confocal techniques continue to provide remarkable clarity and spatial detail of tissue and cellular phenomena. Confocal and electron microscopy provide novel revelations that are now commonplace in medium and large institutions. However, many other cutting-edge technologies and sample preparation workflows are relatively unexploited yet offer tremendous potential for unprecedented advancement in our understanding of the inner workings of pathogenic, beneficial, and symbiotic plant-microbe interactions. Here, we highlight key applications, benefits, and challenges of contemporary advanced imaging platforms for plant-microbe systems with special emphasis on several recently developed approaches, such as light-sheet, single molecule, super-resolution, and adaptive optics microscopy, as well as ambient and cryo-volume electron microscopy, X-ray microscopy, and cryo-electron tomography. Furthermore, the potential for complementary sample preparation methodologies, such as optical clearing, expansion microscopy, and multiplex imaging, will be reviewed. Our ultimate goal is to stimulate awareness of these powerful cutting-edge technologies and facilitate their appropriate application and adoption to solve important and unresolved biological questions in the field. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Kirk J Czymmek
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, U.S.A
- Advanced Bioimaging Laboratory, Donald Danforth Plant Science Center, Saint Louis, MO 63132, U.S.A
| | - Keith E Duncan
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, U.S.A
| | - Howard Berg
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, U.S.A
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Holatko J, Brtnicky M, Mustafa A, Kintl A, Skarpa P, Ryant P, Baltazar T, Malicek O, Latal O, Hammerschmiedt T. Effect of Digestate Modified with Amendments on Soil Health and Plant Biomass under Varying Experimental Durations. MATERIALS (BASEL, SWITZERLAND) 2023; 16:1027. [PMID: 36770034 PMCID: PMC9920836 DOI: 10.3390/ma16031027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/31/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
A digestate with amendments provides plants with available nutrients and improves the microbiological properties of treated soil. Modification of a digestate through the addition of a biochar and sulphur source is less well-known. This pot experiment aimed at comparing the short- and long-time fertilization effects of a digestate enriched with biochar, with elemental sulphur, or with a combination of both on soil health and plant biomass. The experiment was carried out with maize, cultivated twice (1st-12th week = pre-cultivation; re-sowing after shoot harvest, 13th-24th = main cultivation) in soil amended with prepared digestate. The digestate used in pre-cultivation was incubated untreated (D) and was then treated with biochar (D + B), with elemental sulphur at a low (LS) and high (HS) dose, or with a combination of both (D + B + LS and D + B + HS). An additional unamended digestate (D) was added to each soil variant before the main cultivation. The application of digestate with a high dose of elemental sulphur and biochar mediated the most significant differences in the soil. The increase (compared to the unamended soil) was of short-term type (+11% and +6% increased total nitrogen and carbon after 12 weeks), then of long-term type (+54% and +30% increased sulphur and arylsulfatase activity after 24 weeks), and later emerged in the 13th to the 24th week of the experiment (+57% and +32% non-inhibited urease, increased N-acetyl-β-D-glucosaminidase and phosphatase). No significant differences in the effect of the applied amendments on dry aboveground plant biomass were observed.
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Affiliation(s)
- Jiri Holatko
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
- Agrovyzkum Rapotin Ltd., Vyzkumniku 267, 788 13 Rapotin, Czech Republic
| | - Martin Brtnicky
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
- Institute of Chemistry and Technology of Environmental Protection, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic
| | - Adnan Mustafa
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
- Institute of Chemistry and Technology of Environmental Protection, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic
- Institute for Environmental Studies, Faculty of Science, Charles University in Prague, Benatska 2, 128 00 Praha, Czech Republic
| | - Antonin Kintl
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
- Agricultural Research Ltd., Zahradni 400/1, 664 41 Troubsko, Czech Republic
| | - Petr Skarpa
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Pavel Ryant
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Tivadar Baltazar
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Ondrej Malicek
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Oldrich Latal
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
- Agrovyzkum Rapotin Ltd., Vyzkumniku 267, 788 13 Rapotin, Czech Republic
| | - Tereza Hammerschmiedt
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
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Lippold E, Schlüter S, Mueller CW, Höschen C, Harrington G, Kilian R, Gocke MI, Lehndorff E, Mikutta R, Vetterlein D. Correlative Imaging of the Rhizosphere─A Multimethod Workflow for Targeted Mapping of Chemical Gradients. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:1538-1549. [PMID: 36626664 DOI: 10.1021/acs.est.2c07340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Examining in situ processes in the soil rhizosphere requires spatial information on physical and chemical properties under undisturbed conditions. We developed a correlative imaging workflow for targeted sampling of roots in their three-dimensional (3D) context and assessed the imprint of roots on chemical properties of the root-soil contact zone at micrometer to millimeter scale. Maize (Zea mays) was grown in 15N-labeled soil columns and pulse-labeled with 13CO2 to visualize the spatial distribution of carbon inputs and nitrogen uptake together with the redistribution of other elements. Soil columns were scanned by X-ray computed tomography (X-ray CT) at low resolution (45 μm) to enable image-guided subsampling of specific root segments. Resin-embedded subsamples were then analyzed by X-ray CT at high resolution (10 μm) for their 3D structure and chemical gradients around roots using micro-X-ray fluorescence spectroscopy (μXRF), nanoscale secondary ion mass spectrometry (NanoSIMS), and laser-ablation isotope ratio mass spectrometry (LA-IRMS). Concentration gradients, particularly of calcium and sulfur, with different spatial extents could be identified by μXRF. NanoSIMS and LA-IRMS detected the release of 13C into soil up to a distance of 100 μm from the root surface, whereas 15N accumulated preferentially in the root cells. We conclude that combining targeted sampling of the soil-root system and correlative microscopy opens new avenues for unraveling rhizosphere processes in situ.
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Affiliation(s)
- Eva Lippold
- Department of Soil System Science, Helmholtz Centre for Environmental Research - UFZ, Theodor-Lieser-Straße 4, 06120 Halle (Saale), Germany
| | - Steffen Schlüter
- Department of Soil System Science, Helmholtz Centre for Environmental Research - UFZ, Theodor-Lieser-Straße 4, 06120 Halle (Saale), Germany
| | - Carsten W Mueller
- Department of Life Science Systems, Soil Science, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Straße 2, 85354 Freising, Germany
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Øster Voldgade 10, 1350 Copenhagen, Denmark
| | - Carmen Höschen
- Department of Life Science Systems, Soil Science, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Straße 2, 85354 Freising, Germany
| | - Gertraud Harrington
- Department of Life Science Systems, Soil Science, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Straße 2, 85354 Freising, Germany
| | - Rüdiger Kilian
- Mineralogy and Geochemistry, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 3, 06120 Halle (Saale), Germany
| | - Martina I Gocke
- Soil Science and Soil Ecology, Institute of Crop Science and Resource Conservation, University of Bonn, Nussallee 13, 53115 Bonn, Germany
| | - Eva Lehndorff
- Soil Ecology, Bayreuth University, Dr.-Hans-Frisch-Straße 1-3, 95448 Bayreuth, Germany
| | - Robert Mikutta
- Soil Science and Soil Protection, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 3, 06120 Halle (Saale), Germany
| | - Doris Vetterlein
- Department of Soil System Science, Helmholtz Centre for Environmental Research - UFZ, Theodor-Lieser-Straße 4, 06120 Halle (Saale), Germany
- Soil Science and Soil Protection, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 3, 06120 Halle (Saale), Germany
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6
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Rippner DA, Raja PV, Earles JM, Momayyezi M, Buchko A, Duong FV, Forrestel EJ, Parkinson DY, Shackel KA, Neyhart JL, McElrone AJ. A workflow for segmenting soil and plant X-ray computed tomography images with deep learning in Google's Colaboratory. FRONTIERS IN PLANT SCIENCE 2022; 13:893140. [PMID: 36176692 PMCID: PMC9514790 DOI: 10.3389/fpls.2022.893140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 08/12/2022] [Indexed: 06/16/2023]
Abstract
X-ray micro-computed tomography (X-ray μCT) has enabled the characterization of the properties and processes that take place in plants and soils at the micron scale. Despite the widespread use of this advanced technique, major limitations in both hardware and software limit the speed and accuracy of image processing and data analysis. Recent advances in machine learning, specifically the application of convolutional neural networks to image analysis, have enabled rapid and accurate segmentation of image data. Yet, challenges remain in applying convolutional neural networks to the analysis of environmentally and agriculturally relevant images. Specifically, there is a disconnect between the computer scientists and engineers, who build these AI/ML tools, and the potential end users in agricultural research, who may be unsure of how to apply these tools in their work. Additionally, the computing resources required for training and applying deep learning models are unique, more common to computer gaming systems or graphics design work, than to traditional computational systems. To navigate these challenges, we developed a modular workflow for applying convolutional neural networks to X-ray μCT images, using low-cost resources in Google's Colaboratory web application. Here we present the results of the workflow, illustrating how parameters can be optimized to achieve best results using example scans from walnut leaves, almond flower buds, and a soil aggregate. We expect that this framework will accelerate the adoption and use of emerging deep learning techniques within the plant and soil sciences.
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Affiliation(s)
- Devin A. Rippner
- Horticultural Crops Production and Genetic Improvement Research Unit-United States Department of Agriculture-Agricultural Research Service, Prosser, WA, United States
| | - Pranav V. Raja
- Department of Biological and Agricultural Engineering, University of California, Davis, Davis, CA, United States
| | - J. Mason Earles
- Department of Biological and Agricultural Engineering, University of California, Davis, Davis, CA, United States
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - Mina Momayyezi
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - Alexander Buchko
- Department of Computer Science, California Polytechnic and State University, San Luis Obispo, CA, United States
| | - Fiona V. Duong
- Department of Integrative Biology, San Francisco State University, San Francisco, CA, United States
| | - Elizabeth J. Forrestel
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - Dilworth Y. Parkinson
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kenneth A. Shackel
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Jeffrey L. Neyhart
- Genetic Improvement for Fruits and Vegetables Laboratory, United States Department of Agriculture-Agricultural Research Service, Chatsworth, NJ, United States
| | - Andrew J. McElrone
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
- Crops Pathology and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Davis, CA, United States
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