Plant–environment microscopy tracks interactions of Bacillus subtilis with plant roots across the entire rhizosphere

Abstract

Significance The lack of suitable approaches for studying root–microbe interactions, live and in situ, has severely limited our ability to understand the rhizosphere. In this study, we overcome this major limitation with an imaging system that combines transparent soils with cutting edge light sheet microscopy. The study revealed that the root cap is a point of first contact for microbes before establishment and reveals how the pore structure influences the patterns of interactions between the microbe and the plant. With the combined use of light sheet microscopy and transparent soils, we shed light on previously unseen interaction phenomena and accelerate the understanding of how rhizospheres are formed.

Plant phenotyping relevance

透明土壌とライトシート顕微鏡を組み合わせたライブ・インサイチュ画像システムの開発が研究の中心で、根と微生物の相互作用という植物状態を可視化している。

Code and data availability

The paper deposits its phenotyping data (light-sheet microscopy volumes of root–soil–bacteria interactions) on Zenodo, makes its image analysis software (MATLAB/MeVisLab segmentation and quantification pipeline) publicly available on GitHub, and hosts supplementary materials on PNAS.