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Root system architecture and environmental flux analysis in mature crops using 3D root mesocosms
Current methods of root sampling typically only obtain small or incomplete sections of root systems and do not capture their true complexity. To facilitate the visualization and analysis of full-sized plant root systems in 3-dimensions, we developed customized mesocosm growth containers. While highl...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9800027/ https://www.ncbi.nlm.nih.gov/pubmed/36589101 http://dx.doi.org/10.3389/fpls.2022.1041404 |
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author | Dowd, Tyler G. Li, Mao Bagnall, G. Cody Johnston, Andrea Topp, Christopher N. |
author_facet | Dowd, Tyler G. Li, Mao Bagnall, G. Cody Johnston, Andrea Topp, Christopher N. |
author_sort | Dowd, Tyler G. |
collection | PubMed |
description | Current methods of root sampling typically only obtain small or incomplete sections of root systems and do not capture their true complexity. To facilitate the visualization and analysis of full-sized plant root systems in 3-dimensions, we developed customized mesocosm growth containers. While highly scalable, the design presented here uses an internal volume of 45 ft(3) (1.27 m(3)), suitable for large crop and bioenergy grass root systems to grow largely unconstrained. Furthermore, they allow for the excavation and preservation of 3-dimensional root system architecture (RSA), and facilitate the collection of time-resolved subterranean environmental data. Sensor arrays monitoring matric potential, temperature and CO(2) levels are buried in a grid formation at various depths to assess environmental fluxes at regular intervals. Methods of 3D data visualization of fluxes were developed to allow for comparison with root system architectural traits. Following harvest, the recovered root system can be digitally reconstructed in 3D through photogrammetry, which is an inexpensive method requiring only an appropriate studio space and a digital camera. We developed a pipeline to extract features from the 3D point clouds, or from derived skeletons that include point cloud voxel number as a proxy for biomass, total root system length, volume, depth, convex hull volume and solidity as a function of depth. Ground-truthing these features with biomass measurements from manually dissected root systems showed a high correlation. We evaluated switchgrass, maize, and sorghum root systems to highlight the capability for species wide comparisons. We focused on two switchgrass ecotypes, upland (VS16) and lowland (WBC3), in identical environments to demonstrate widely different root system architectures that may be indicative of core differences in their rhizoeconomic foraging strategies. Finally, we imposed a strong physiological water stress and manipulated the growth medium to demonstrate whole root system plasticity in response to environmental stimuli. Hence, these new “3D Root Mesocosms” and accompanying computational analysis provides a new paradigm for study of mature crop systems and the environmental fluxes that shape them. |
format | Online Article Text |
id | pubmed-9800027 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-98000272022-12-30 Root system architecture and environmental flux analysis in mature crops using 3D root mesocosms Dowd, Tyler G. Li, Mao Bagnall, G. Cody Johnston, Andrea Topp, Christopher N. Front Plant Sci Plant Science Current methods of root sampling typically only obtain small or incomplete sections of root systems and do not capture their true complexity. To facilitate the visualization and analysis of full-sized plant root systems in 3-dimensions, we developed customized mesocosm growth containers. While highly scalable, the design presented here uses an internal volume of 45 ft(3) (1.27 m(3)), suitable for large crop and bioenergy grass root systems to grow largely unconstrained. Furthermore, they allow for the excavation and preservation of 3-dimensional root system architecture (RSA), and facilitate the collection of time-resolved subterranean environmental data. Sensor arrays monitoring matric potential, temperature and CO(2) levels are buried in a grid formation at various depths to assess environmental fluxes at regular intervals. Methods of 3D data visualization of fluxes were developed to allow for comparison with root system architectural traits. Following harvest, the recovered root system can be digitally reconstructed in 3D through photogrammetry, which is an inexpensive method requiring only an appropriate studio space and a digital camera. We developed a pipeline to extract features from the 3D point clouds, or from derived skeletons that include point cloud voxel number as a proxy for biomass, total root system length, volume, depth, convex hull volume and solidity as a function of depth. Ground-truthing these features with biomass measurements from manually dissected root systems showed a high correlation. We evaluated switchgrass, maize, and sorghum root systems to highlight the capability for species wide comparisons. We focused on two switchgrass ecotypes, upland (VS16) and lowland (WBC3), in identical environments to demonstrate widely different root system architectures that may be indicative of core differences in their rhizoeconomic foraging strategies. Finally, we imposed a strong physiological water stress and manipulated the growth medium to demonstrate whole root system plasticity in response to environmental stimuli. Hence, these new “3D Root Mesocosms” and accompanying computational analysis provides a new paradigm for study of mature crop systems and the environmental fluxes that shape them. Frontiers Media S.A. 2022-12-15 /pmc/articles/PMC9800027/ /pubmed/36589101 http://dx.doi.org/10.3389/fpls.2022.1041404 Text en Copyright © 2022 Dowd, Li, Bagnall, Johnston and Topp https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Plant Science Dowd, Tyler G. Li, Mao Bagnall, G. Cody Johnston, Andrea Topp, Christopher N. Root system architecture and environmental flux analysis in mature crops using 3D root mesocosms |
title | Root system architecture and environmental flux analysis in mature crops using 3D root mesocosms |
title_full | Root system architecture and environmental flux analysis in mature crops using 3D root mesocosms |
title_fullStr | Root system architecture and environmental flux analysis in mature crops using 3D root mesocosms |
title_full_unstemmed | Root system architecture and environmental flux analysis in mature crops using 3D root mesocosms |
title_short | Root system architecture and environmental flux analysis in mature crops using 3D root mesocosms |
title_sort | root system architecture and environmental flux analysis in mature crops using 3d root mesocosms |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9800027/ https://www.ncbi.nlm.nih.gov/pubmed/36589101 http://dx.doi.org/10.3389/fpls.2022.1041404 |
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