Digitally Deconstructing Leaves in 3D Using X-ray Microcomputed Tomography and Machine Learning

Théroux‐Rancourt, Guillaume; Jenkins, Matthew R.; Brodersen, Craig R.; McElrone, Andrew J.; Forrestel, Elisabeth J.

doi:10.1101/814954

Cited by 7 publications

(12 citation statements)

References 16 publications

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“…(b) MicroCT data acquisition Images were reconstructed using TomoPy [54] for all ALS samples or using the in-house reconstruction platform for SLS or APS samples. Reconstructed scans were processed using published methods [32,55], and image stacks were cropped to remove tissue that was dehydrated, damaged or contained artefacts from the imaging or reconstruction steps. The final stacks contained approximately 500-2000 eight-bit grayscale images (downsampled from 16 or 32-bit images).…”

Section: Materials and Methods (A) Plant Materialsmentioning

confidence: 99%

“…To extract surface area and volumes, mesophyll cells, airspace, vasculature (combined veins and bundle sheath) and background (including the epidermis) were segmented using published methods [32,55] and ImageJ [57]. Airspace volume (V pores ), mesophyll cell volume (V cells ), both summing up to the total mesophyll volume (V mes ), vasculature volume (V veins ) and the surface area exposed to the intercellular airspace (SA mes ) were then extracted using published methods [32] with the ImageJ plugin BoneJ [58], or using a custom Python program [55] (https://github.com/plant-microcttools/leaf-traits-microct). SA mes /V mes is less sensitive to leaf thickness than the commonly measured S m , i.e.…”

Section: Materials and Methods (A) Plant Materialsmentioning

confidence: 99%

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Maximum CO₂diffusion inside leaves is limited by the scaling of cell size and genome size

et al. 2021

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Maintaining high rates of photosynthesis in leaves requires efficient movement of CO 2 from the atmosphere to the mesophyll cells inside the leaf where CO 2 is converted into sugar. CO 2 diffusion inside the leaf depends directly on the structure of the mesophyll cells and their surrounding airspace, which have been difficult to characterize because of their inherently three-dimensional organization. Yet faster CO 2 diffusion inside the leaf was probably critical in elevating rates of photosynthesis that occurred among angiosperm lineages. Here we characterize the three-dimensional surface area of the leaf mesophyll across vascular plants. We show that genome size determines the sizes and packing densities of cells in all leaf tissues and that smaller cells enable more mesophyll surface area to be packed into the leaf volume, facilitating higher CO 2 diffusion. Measurements and modelling revealed that the spongy mesophyll layer better facilitates gaseous phase diffusion while the palisade mesophyll layer better facilitates liquid-phase diffusion. Our results demonstrate that genome downsizing among the angiosperms was critical to restructuring the entire pathway of CO 2 diffusion into and through the leaf, maintaining high rates of CO 2 supply to the leaf mesophyll despite declining atmospheric CO 2 levels during the Cretaceous.

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Section: Materials and Methods (A) Plant Materialsmentioning

confidence: 99%

Section: Materials and Methods (A) Plant Materialsmentioning

confidence: 99%

Maximum CO₂diffusion inside leaves is limited by the scaling of cell size and genome size

et al. 2021

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“…Three-dimensional anatomy and stomatal traits. We extracted the volume and surface area of leaf anatomical traits from the full segmented stacks 52 . We estimated the volumes of the epidermis (Vep), bundle sheath and transfusion tissue (VBS+TT), mesophyll cells (Vcell), mesophyll intercellular airspace (VIAS), resin ducts (Vresin), and veins (Vvein).…”

Section: Methodsmentioning

confidence: 99%

The 3D construction of leaves is coordinated with water use efficiency in conifers

Trueba

Théroux‐Rancourt

Buckley

et al. 2021

Preprint

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Conifers prevail in the canopies of many terrestrial biomes, holding a great ecological and economic importance globally. Current increases in temperature and aridity are resulting in conifer mortality and imposing high transpirational demands to global vegetation. Therefore, identifying leaf structural determinants of carbon acquisition and water use efficiency is essential in predicting physiological impacts due to environmental variation. Using synchrotron-generated microCT imaging, we extracted leaf volumetric anatomy and stomatal traits in 34 species across the conifers with a special focus on Pinus, the richest conifer genus. We show that intrinsic water use efficiency (WUEi) is driven by leaf vein volume, with both traits scaling positively. The ratios of stomatal pore number per unit mesophyll or intercellular airspace volume emerged as powerful explanatory variables, accurately predicting both stomatal conductance and WUEi. Our results clarify how the three-dimensional organization of tissues within the leaf has a direct impact on plant water use and carbon uptake

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“…To extract surface area and volumes, the final image stacks were first segmented using manual or automated methods of Théroux-Rancourt et al 26,48 to segment the mesophyll cells, the airspace, the vasculature (combined veins and bundle sheath), and the background (including the epidermis). For both methods, ImageJ 49 was used to segment or prepare the image stacks for segmentation.…”

Section: Leaf Trait Analysismentioning

confidence: 99%

Maximum CO₂diffusion inside leaves is limited by the scaling of cell size and genome size

Théroux‐Rancourt

Roddy

Gilbert

et al. 2020

Preprint

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SummaryMaintaining high rates of photosynthesis in leaves requires efficient movement of CO2 from the atmosphere to the chloroplasts inside the leaf where it is converted into sugar. Throughout the evolution of vascular plants, CO2 diffusion across the leaf surface was maximized by reducing the sizes of the guard cells that form stomatal pores in the leaf epidermis1,2. Once inside the leaf, CO2 must diffuse through the intercellular airspace and into the mesophyll cells where photosynthesis occurs3,4. However, the diffusive interface defined by the mesophyll cells and the airspace and its coordinated evolution with other leaf traits are not well described5. Here we show that among vascular plants variation in the total amount of mesophyll surface area per unit mesophyll volume is driven primarily by cell size, the lower limit of which is defined by genome size. The higher surface area enabled by smaller cells allows for more efficient CO2 diffusion into photosynthetic mesophyll cells. Our results demonstrate that genome downsizing among the flowering plants6 was critical to restructuring the entire pathway of CO2 diffusion, facilitating high rates of CO2 supply to the leaf mesophyll cells despite declining atmospheric CO2 levels during the Cretaceous.

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Digitally Deconstructing Leaves in 3D Using X-ray Microcomputed Tomography and Machine Learning

Cited by 7 publications

References 16 publications

Maximum CO₂diffusion inside leaves is limited by the scaling of cell size and genome size

Maximum CO₂diffusion inside leaves is limited by the scaling of cell size and genome size

The 3D construction of leaves is coordinated with water use efficiency in conifers

Maximum CO₂diffusion inside leaves is limited by the scaling of cell size and genome size

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Digitally Deconstructing Leaves in 3D Using X-ray Microcomputed Tomography and Machine Learning

Cited by 7 publications

References 16 publications

Maximum CO2diffusion inside leaves is limited by the scaling of cell size and genome size

Maximum CO2diffusion inside leaves is limited by the scaling of cell size and genome size

The 3D construction of leaves is coordinated with water use efficiency in conifers

Maximum CO2diffusion inside leaves is limited by the scaling of cell size and genome size

Contact Info

Product

Resources

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Maximum CO₂diffusion inside leaves is limited by the scaling of cell size and genome size

Maximum CO₂diffusion inside leaves is limited by the scaling of cell size and genome size

Maximum CO₂diffusion inside leaves is limited by the scaling of cell size and genome size