Abstract
Plant growth is supported by complex interactions with many biophysical elements of their environment including microorganisms, geochemicals, water and gas, all within the otherwise complex and heterogeneous soils’ physical environment. Our understanding of plant-environment interactions in soil is limited by the difficulty of observing such interactions at the microscopic scale which occur throughout the large volume of influence of the plant.This thesis presents the development of 3D live microscopy approaches for resolving plant-microbe interactions across the environment of an entire seedling root growing in a transparent soil in tailor-made microcosms with water, nutrients, and atmosphere. The thesis studies the suitability of artificial soils, designs and fabrication of microcosm chamber, and control of fluids that can provide physical conditions for the co-culture of plant-microorganism system and access to optical imaging. To study biological activity in such microcosms a dualillumination light-sheet system was developed to acquire light scattering signals from the plant whilst fluorescence signals were captured from the transparent soil particles and labelled microorganisms, allowing the generation of volumetric and multispectral time-lapse data from samples up to 3600 mm3 in size with best resolution of 5 µm and fastest rate of one scan every 15 minutes. The acquired raw images were processed by a customised processing pipeline to enhance useful information and extract 3D geometry of the rhizosphere for quantitatively analysis and visualisation. Additionally, the thesis showed the feasibility of predicting plant induced pH changes using machine learning algorithm utilising the multispectral signals from the pH-sensitive soil provided by SENSOIL project. To my knowledge, the first in situ measurement of pH in the rhizosphere at micro scale was achieved.
This thesis delivers integrated live microscopy systems to observe dynamical processes in the plant environment. It can track 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 transparent soil particles, colonising the root in a pulsatile manner. Migrations appeared to be directed first towards the root cap as the point “first contact”, before subsequent colonisation of mature epidermis cells. Findings in this thesis show that environmental microscopes present an invaluable tool to understand life in soils.
| Date of Award | 2021 |
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| Original language | English |
| Awarding Institution |
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| Supervisor | Michael MacDonald (Supervisor) & Lionel Xavier Dupuy (Supervisor) |