U.S. Department of Energy

Pacific Northwest National Laboratory

How Plant Roots Take Up Water from Soil

The computational domain (0.03 m x 0.03 m x 0.0063 m) and the simulation setup. The three-dimensional root structure, with the same imaging resolution, is in the middle, surrounded by soils.

The Science 

Root water uptake is one of the most important processes in subsurface flow and transport modeling. It is driven by transpiration caused by the water potential gradient between the atmosphere and the plant. But the mechanisms of root water uptake are poorly known, and are represented only coarsely in macro-scale models because of the difficulties of both imaging and modeling such systems.

A new paper in the journal Rhizosphere, by Timothy D. Scheibe and three co-authors at the Pacific Northwest National Laboratory (PNNL), demonstrates a promising way to address those difficulties. In a pilot study, they successfully simulate three-dimensional root water uptake by applying a combination of X-ray Computed Tomography (XCT) and computational fluid dynamics (CFD) modeling at the pore-scale.

The Impact

The new coupled imaging-modeling approach introduces a realistic platform for investigating rhizosphere flow processes – one that could support translation of process understanding from a single-plant to vegetation scales. The same imaging-modeling method could also be used to simulate more realistic scenarios and compared to laboratory and field plot studies to improve process understanding.


Successful in-soil imaging of a live plant could unlock mysteries regarding the complex plant-soil-microbe interactions in the rhizosphere. This plant-root interface, teeming with microorganisms and bathed in water at every scale, is where complex chemical, biological, and physical interactions determine the health of plants, their root systems, and the surrounding soil.

To date, however, imaging and modeling root water uptake has been difficult. The complexity of the root architecture and soil properties makes explicit imaging problematic. Estimating plant-root and soil properties for modeling is also difficult, compounded by a poor understanding of the hydrological and biological processes involved in root water uptake.

In the last decade, a promising series of papers has shown the potential of integrating high-resolution imaging techniques and pore-scale modeling for investigating the interactions of soil, roots, and groundwater.

A team at PNNL recently combined non-invasive XCT imaging with both open-source and in-house software codes. They successfully imaged root water uptake at a micron-scale resolution in 3D and they also modeled the spatiotemporal variations of water uptake. What they call a “pioneer” pilot study provides a platform for future research into the role of plant roots in nutrient uptake, hydraulic redistribution, and other phenomena in the rhizosphere.

The researchers used a single Prairie dropseed (Sporobolus heterolepis) plant grown in a pot, which was rotated continuously during a scan that captured 3,142 projections (at four frames per projection). The raw images were used to create a three-dimensional dataset. From there, in-house PNNL softwarederived quantitative information, including root volume and surface area. The result was a mechanistic pore-scale numerical model of root uptake processes. 

The study showed that soil water distribution was controlled by both plant-root and soil conductivity, and by transpiration rate. But more broadly, it demonstrated a realistic platform for investigating rhizosphere flow processes.


This research was supported by the U.S. Department of Energy (DOE) Biological and Environmental Research (BER) Division through the Terrestrial Ecosystem Science (TES) program and the Subsurface Biogeochemical Research (SBR) program, through the PNNL SBR Scientific Focus Area Project. Part of this research was performed at the Environmental Molecular Sciences Laboratory (EMSL), a DOE scientific user facility located at Pacific Northwest National Laboratory (PNNL).


X Yang et al., “What can we learn from in-soil imaging of a live plant: X-ray Computed Tomography and 3D numerical simulation of root soil system.” RhizosphereVol. 3 Part 2, June 2017, 259-262. DOI: 10.1016/j.rhizosph.2017.04.017

Related Links 



June 2017
| Pacific Northwest National Laboratory