Opening the black box: in situ imaging of arbuscular mycorrhizal fungal structures in soil using synchrotron‐based micro‐ CT
Abstract
Arbuscular mycorrhizal fungi (AMF) contribute to plant nutrient and water uptake via their extraradical hyphal networks. However, in situ methodologies to quantify architectural and morphological traits of these networks in soil are largely lacking, limiting our understanding of AMF-mediated resource transport.
Using synchrotron-based X-ray computed microtomography (micro-CT), we established a workflow to cultivate, noninvasively image, and quantitatively analyze AMF hyphosphere and rhizosphere structures in the interaggregate space across two soil textures and biological contexts.
We developed a pipeline for quantitative three-dimensional (3D) assessment of key architectural and morphological traits including structure counts, hyphal length, branching frequency, volume, and surface area. Our method further permits (1) measurement of AMF-soil and AMF-root interface areas and (2) microscale quantification of pore space occupancy by AMF.
Micro-CT offers a tool for noninvasively visualizing AMF in air-filled soil pore space. We outline how such quantitative 3D information can be incorporated into image-based and functional-structural soil-plant models, thereby supporting a better mechanistic understanding of AMF-mediated processes in soils and plants.
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BibTeX
@article{braunmiller2026opening,
title = {{Opening the black box: in situ imaging of arbuscular mycorrhizal fungal structures in soil using synchrotron‐based micro‐ CT}},
author = {Henri M Braunmiller and Michael Bitterlich and Nicolai Koebernick and Eva Jacob and Anna S Heck and Andrea Schnepf and Johanna Pausch and Jussi‐petteri Suuronen and Bernhard Hesse and Sylvain Delzon and Jonathan Perrin and Andrew King and Jan Jansa and Mutez A Ahmed},
journal = {New Phytologist},
year = {2026},
month = jul,
doi = {10.1111/nph.71379},
url = {https://hal.inrae.fr/hal-05798783v1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Opening the black box: in situ imaging of arbuscular mycorrhizal fungal structures in soil using synchrotron‐based micro‐ CT
AU - Henri M Braunmiller
AU - Michael Bitterlich
AU - Nicolai Koebernick
AU - Eva Jacob
AU - Anna S Heck
AU - Andrea Schnepf
AU - Johanna Pausch
AU - Jussi‐petteri Suuronen
AU - Bernhard Hesse
AU - Sylvain Delzon
AU - Jonathan Perrin
AU - Andrew King
AU - Jan Jansa
AU - Mutez A Ahmed
PY - 2026
DA - 2026/07/02
JO - New Phytologist
DO - 10.1111/nph.71379
UR - https://hal.inrae.fr/hal-05798783v1
AB - Arbuscular mycorrhizal fungi (AMF) contribute to plant nutrient and water uptake via their extraradical hyphal networks. However, in situ methodologies to quantify architectural and morphological traits of these networks in soil are largely lacking, limiting our understanding of AMF-mediated resource transport. Using synchrotron-based X-ray computed microtomography (micro-CT), we established a workflow to cultivate, noninvasively image, and quantitatively analyze AMF hyphosphere and rhizosphere structures in the interaggregate space across two soil textures and biological contexts. We developed a pipeline for quantitative three-dimensional (3D) assessment of key architectural and morphological traits including structure counts, hyphal length, branching frequency, volume, and surface area. Our method further permits (1) measurement of AMF-soil and AMF-root interface areas and (2) microscale quantification of pore space occupancy by AMF. Micro-CT offers a tool for noninvasively visualizing AMF in air-filled soil pore space. We outline how such quantitative 3D information can be incorporated into image-based and functional-structural soil-plant models, thereby supporting a better mechanistic understanding of AMF-mediated processes in soils and plants.
SN - 0028-646X
SN - 1469-8137
ER -