Electron Microscopy for Plant Biology and Crop Sciences

Electron microscopy for structural insights into plant cell biology and crop science research

Structural biology techniques, with their ability to unravel the 3D architecture of macromolecules, have played a crucial role in deciphering various physiological activities of plants at the molecular level. Ultrastructural investigations using electron microscopy can provide biological insight across orders of magnitude in length, from high-resolution macromolecular structures to volumetric techniques that reveal the 3D ultrastructural organization of cells and tissues.

 

These techniques can help you obtain remarkable structural insights into photosynthesis efficiency and crop yields, plant-microbe interactions, viral infections in plants, plant development and stress responses, crop improvement for sustainable agriculture, and more.

Cryo-electron microscopy of 3D macromolecular structures

Cryo-electron microscopy (cryo-EM) single particle analysis can help you collect near atomic-resolution information of macromolecules at near-native conditions. Gain a visual understanding of the biochemistry in your samples for new insights that move your research forward.

Cryo-EM structure of the photosynthesis protein PSI in state 1 (PSI- ST1) from Arabidopsis thaliana at 3.06 Å resolution

Plants are known to react to changing environmental light conditions, but the mechanisms behind this response were not always fully understood. Wu et al. obtained novel structural and functional insights into the mechanisms of light acclimation during state transitions in Arabidopsis thaliana using single particle cryo-EM. Previously, these regulatory pathways underlying state transitions were not known for higher plants.[i]

Cryo-EM structure of the photosynthesis protein PSI in state 1 (PSI-ST1) from Arabidopsis thaliana at 3.06 Å resolution. PDB ID: 8J7A

Cryo-electron tomography (cryo-ET) puts visualization of macromolecules into the context of a cellular landscape to help you understand the localization of your particles of interest within cellular compartments as well as their interactions with other macromolecules, signaling complexes, viruses, and microbes in near-native conditions.

Cryo-EM studies of the insecticidal Vip3Bc1 tetramer from B. thuringiensis

In this example, researchers used cryo-EM and cryo-ET methods to investigate the mechanism of action of vegetative insecticidal protein 3 (Vip3), a cutting-edge method of pest control where transgenic plants create their own defenses against crop pests.[ii]

 

Thermo Fisher Scientific offers a family of cryo-TEM systems with cryo-EM and cryo-ET capabilities. Whether you are new to cryo-electron microscopy and starting your journey of discovery or part of an advanced structural biology facility, our instruments were developed to meet your unique needs.

Cryo-EM structure of the Vip3Bc1 tetramer from B. thuringiensis at 3.9 Å resolution. PDB ID: 6YRF. Inset image is Vip3Bc1 directly visualized on liposome membranes. Segmented density from cryo-ET shows interaction of Vip3Bc1 (colored) with the LUV membrane (white). Figure reproduced under CC-BY 4.0

Ultrastructural SEM and TEM imaging

Scanning electron microscopy (SEM) and transmission electron  microscopy (TEM) allow you to explore cellular structures at the nanoscale range. From the first electron microscopy images of mitochondria, chloroplasts, and plant cell walls that were collected over sixty years ago[iii], technology improvements have continued to advance over the decades, providing higher automation for more efficient workflows and ever clearer and more insightful visualizations of the inner structures and organelles of plant cells and their interactions with microbes and viruses.

Cross section of a tobacco leaf, stained and embedded in Quetol resin. Sample courtesy of Dr. Kirk J. Czymmek, Principal Investigator, Director Advanced Bioimaging Laboratory, Donald Danforth Plant Science Center, USA.

SEM and TEM systems can be equipped now, or in the future, with the following capabilities to grow with your facility:

  • Correlative electron microscopy (CLEM) to combine fluorescence microscopy and nanometer-resolution structural electron microscopy imaging to help you target specific areas of interest. J.M. Dragwidge et al. used CLEM to investigate clathrin-mediated endocytosis in plants.[iv]
  • Array tomography to capture intracellular structures in 3D. Y. Cui et al. performed 3D electron tomography to investigate vacuole biogenesis in Arabidopsis root cells.[v]

 

Thermo Scientific SEMs and TEMs deliver outstanding imaging quality and upgrade paths to ensure your system delivers the data you need now and is ready for experiments you may design in the future.

3D volumetric SBF-SEM and FIB-SEM imaging

Volume electron microscopy (vEM) encompasses a range of techniques that capture a series of 2D ultra-resolution electron microscopy images to create a 3D image of a sample that can range from a micrometer up to a millimeter in size at nanometer resolution.[vi] Volume electron microscopy can reconstruct intracellular structures up through entire cells and millimeters of tissue samples, unlocking the minute details of structural relationships at previously impossible length scales.

Overview of plasmodesmal connections in the phloem region of a plant tumor

Lv et al. used high-throughput volume electron microscopy, including FIB-SEM, to show that sieve plate pores and flexible gateways of the phloem have a sufficiently large size exclusion limit (SEL) to accommodate virions and potentially serve as pathways for virion movement.[vii]

Overview of all plasmodesmal connections in the phloem region of a plant tumor. Figure reproduced under CC BY-ND 4.0.

Alternatively, serial block-face scanning electron microscopy (SBF-SEM) incorporates an ultramicrotome directly in the chamber of an SEM to automate slicing resin-embedded samples and subsequent imaging of the exposed block face. The high level of automation enables acquisition of a larger sample size. Kalmbach et al. used SBF-SEM to study PLL12 in young roots to understand its function in differentiation of sieve element cells, which are required for the distribution of photosynthesis products by the phloem.[viii] For higher precision, plasma focused ion beam SEM (PFIB-SEM) enables high-throughput, higher-resolution volume electron microscopy at room temperature or under cryogenic conditions. The ion beam accurately mills away the sample as the SEM images the revealed surface.

3D Rendering of green algae Chlamydomonas organelles

Czymmek et al. describe a range of routinely performed microscopy techniques used to explore cell biology in plants and other organisms. They highlight emerging electron microscopy and cryo-EM technologies, including cryo-FIB-SEM, that have a particular potential to expand our understanding of plant structure and function as well as plant-pathogen interactions.[ix] In this image of green algae Chlamydomonas organelles, they show the chloroplast and its thylakoid membranes (purple), pyrenoid tubules (orange), Golgi (yellow), and nucleus (cyan).

3D rendering of the green algae Chlamydomonas organelles showing the chloroplast and its thylakoid membranes (purple), pyrenoid tubules (orange), Golgi (yellow), and nucleus (cyan). Scale bars = 1 µm. Dataset acquired on a Thermo Scientific Helios Hydra Plasma FIB-SEM. Figure reproduced under CC BY 4.0.

FIB-SEM enables crop science research at Donald Danforth Plant Science Center

“We are increasingly being challenged to understand how to improve crop resilience to environmental stress and disease. The remarkable capabilities of our new Thermo Scientific Hydra Bio Plasma-FIB will allow us the unprecedented ability to reconstruct entire plant cells and tissue with exquisite detail. This technology will allow us to ‘freeze’ organisms in time and space and build intricate 3D models that will help us solve our critical food security challenges.”

 

Kirk J. Czymmek, Principal Investigator, Director Advanced Bioimaging Laboratory, Donald Danforth Plant Science Center

Looking for proof of concept? Our applications team can help

Our global team is here to help you understand how our systems will benefit your research. From imaging samples sent from your laboratory for initial data collection to receiving you as a visitor for a hands-on experience, our NanoPort facilities are here to support your journey to discovery with electron microscopy. We encourage you to have a conversation with our global applications team to see how we can help you coordinate your next step, from sending us your samples to planning your visit.

Plant biology resources

eBook: Novel insights into plant biology with electron microscopy

Plant biology sample images

SEM image of a transversal cut of flower cells.
SEM image of a pollen grain surface. Image courtesy of Mrs. Seydanur Kaya, Kastamonu University.
SEM image of a pollen grain surface.
SEM image of a pollen grain surface. Image courtesy of Mrs. Seydanur Kaya, Kastamonu University.
Cryo-TEM image of an Arabidopsis leaf.
Cryo-TEM image of an Arabidopsis leaf where the seedling was grown in total darkness. Crystalline prolamellar bodies within the etioplasts are visible. Image courtesy of Ms. Pat Kysar, University of California, Davis.

References

[i] Wu, J, et al. Regulatory dynamics of higher plant PSI-LHCI supercomplex during state transition. Molecular Plant 6:12 p1937–1950, (2023). https://doi.org/10.1016/j.molp.2023.11.002

[ii]  Byrne, MJ, et al. Cryo-EM structures of an insecticidal Bt toxin reveal its mechanism of action on the membrane. Nat Commun 12:2791, (2021). https://doi.org/10.1038/s41467-021-23146-4

[iii]  Sjöstrand, F. S. (1956). "Electron Microscopy of Cells and Tissues."

[iv] Dragwidge, J.M., et al. Biomolecular condensation orchestrates clathrin-mediated endocytosis in plants. Nature Cell Biology 26, 438–449 (2024). https://doi.org/10.1038/s41556-024-01354-6

[v]  Cui, Y., et al. A whole-cell electron tomography model of vacuole biogenesis in Arabidopsis root cells. Nature Plants 5, 95–105 (2019). https://doi.org/10.1038/s41477-018-0328-1

[vi] Collinson, L.M., et al. Volume EM: a quiet revolution takes shape. Nature Methods 20, 777–782, (2023). https://doi.org/10.1038/s41592-023-01861-8

[vii]  Lv, M, et al. Volume electron microscopy reconstruction uncovers a physical barrier that limits virus to phloem. New Phytologist 241 p343–362, 2024. https://doi.org/10.1111/nph.19319

[viii]  Kalmbach, L, et al. Putative pectate lyase PLL12 and callose deposition through polar CALS7 are necessary for long-distance phloem transport in Arabidopsis. Current Biology 33:5 p926-939.e9, (2023). https://doi.org/10.1016/j.cub.2023.01.038

[ix]  Czymmek, KJ, et al. Realizing the Full Potential of Advanced Microscopy Approaches for Interrogating Plant-Microbe Interactions. MPMI 36:4 p245-255, 2023. https://doi.org/10.1094/MPMI-10-22-0208-FI

For Research Use Only. Not for use in diagnostic procedures.