Visualizing intact microscopic structures around plant roots

May 20, 2026

Electron microscopy to observe intact configuration of plants, microbes, and soil

Researchers at RIKEN CSRS have developed an electron microscopy technique that enables the observation of the rhizosphere, the area surrounding plant roots where microbes and soil minerals intermingle, over a wide range and with subcellular-level detail.

In the rhizosphere, plants, microorganisms, organic substances, and soil minerals are in contact intricately. Because biological samples are soft and soil minerals are hard, it was difficult to observe a wide intact area with roots and soil using conventional microtomy for electron microscopy.

In this study, the research team established the biological cross-sectional polishing scanning electron microscopy (bioCP-SEM). This technique combines fixation and resin embedding for biological samples with cross-sectional polishing for material observation. A sample in which the whole rhizosphere is embedded is sliced and polished. The polished cross-section is then examined using a scanning electron microscope.

This method enables the observation of microbial clusters, biofilm-like structures, mycelial networks, and protist-like structures in field-collected rhizosphere samples, while preserving the original geometry of plant tissues and minerals.

The findings of this research are expected to help deepen understanding of the interaction between plants and soil microbes and establish the underlying technology for analyzing rhizosphere structures in studies of agricultural production and environmental responses.

 

Original article

Communications Earth & Environment　doi: 10.1038/s43247-026-03598-6

K. Toyooka, Y. Saito, S. Kojima, Y. Goto, M. Sato,

"Biological cross-sectional polishing scanning electron microscopy enables wide-area ultrastructural mapping of intact plant-microbe-soil interfaces".

Contact

Kiminori Toyooka
Senior Technical Scientist
Mass Spectrometry and Microscopy Unit