Root system architecture and environmental flux analysis in mature crops using 3D root mesocosms

Abstract

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 ft3 (1.27 m3), 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 CO2 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.

Comparison of open‐source three‐dimensional reconstruction pipelines for maize‐root phenotyping

“…The use of 3D imaging techniques in root phenotyping is promising because of their ability to leverage multiple views of a given scene to resolve occlusion in dense root architectures (Bucksch, 2014; Clark et al., 2011; Dowd et al., 2022; Topp et al., 2013). However, 3D imaging methods, such as X‐ray CT (Shao et al., 2021) or magnetic resonance imaging (MRI; van Dusschoten et al., 2016), are 100–1000 times more expensive than multicamera systems (Liu et al., 2021), and do not meet the needs of large‐scale field studies due to the high operation cost and difficulties in deploying in the field environment.…”