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

Yangminghao Liu, Daniel Patko, Ilonka Engelhardt, Timothy S. George, Nicola Stanley-Wall, Vincent Ladmiral, Bruno Ameduri, Tim J. Daniell, Nicola Holden, Michael P. MacDonald (Lead / Corresponding author), Lionel X. Dupuy (Lead / Corresponding author)

Research output: Contribution to journalArticlepeer-review

21 Citations (Scopus)
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Our understanding of plant-microbe interactions in soil is limited by the difficulty of observing processes at the microscopic scale throughout plants’ large volume of influence. Here, we present the development of 3D live microscopy for resolving plant-microbe interactions across the environment of an entire seedling growing in a transparent soil in tailor-made mesocosms, maintaining physical conditions for the culture of both plants and microorganisms. A tailor made dual-illumination light-sheet system acquired photons scattered from the plant whilst fluorescence emissions were simultaneously captured from transparent soil particles and labelled microorganisms, allowing the generation of quantitative data on samples approximately 3600 mm3 in size with as good as 5 µm resolution at a rate of up to one scan every 30 minutes. The system tracked the movement of Bacillus subtilis populations in the rhizosphere of lettuce plants in real time, revealing previously unseen patterns of activity. Motile bacteria favoured small pore spaces over the surface of soil particles, colonising the root in a pulsatile manner. Migrations appeared to be directed towards the root cap, the point of “first contact”, before subsequent colonisation of mature epidermis cells. Our findings show that microscopes dedicated to live environmental studies present an invaluable tool to understand plant-microbe interactions.
Original languageEnglish
Article numbere2109176118
Number of pages8
JournalProceedings of the National Academy of Sciences
Issue number48
Publication statusPublished - 30 Nov 2021


  • environmental imaging
  • root-microbe interactions
  • rhizosphere


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