Microbes-on-a-chip: deciphering the responsiveness of microbes using microfluidic chemostats
File(s)
Author(s)
Bernier, Léa Suzanne
Type
Thesis
Abstract
Soil is essential for all forms of life. Highly complex and heterogeneous, it contains immense biodiversity: plants, fungi, bacteria, and more. Interestingly, the vast majority of bacteria in soil lie dormant. Specific germinants can reactivate some of these metabolically inactive spores. Similarly, some fungi also form diverse spores. Understanding this germination process is crucial for sustainable agriculture, as these spores interact with plants and other microbes and could be used as biocontrol agents. The main objective of this thesis was to develop a tool to observe and measure the germination of microbial spores in the presence of different germinants.
Microfluidics technologies refer to devices that handle fluids at the micrometre scale. They allow for continuous monitoring of individual cells over long periods, revealing behaviours that would be masked when looking only at the population level or only at snapshots.
The main microfluidic device developed in this thesis, called the 4-Conditions Microfluidic Chemostat (4CMC), consists of an array of microchemostats exposed to four different environmental conditions. It was validated through a series of experiments with the model organism Bacillus subtilis, which revealed new insights into the effect of spore density on spore germination. The device was also used to elucidate the responsiveness of spores of two non-model soil dwellers, the bacterium Ammoniphilus oxalaticus and the fungus Trichoderma rossicum, both of which are potential biocontrol agents. This research led to new findings on A. oxalaticus spores' response to oxalate, an abundant component of soil, and on the effect of nutrient availability on T. rossicum spores.
The 4CMC was also employed to study the responsiveness of engineered bacteria and yeast communities, revealing behaviours that standard population-level assays had masked, as well as choanoflagellates.
Microfluidics technologies refer to devices that handle fluids at the micrometre scale. They allow for continuous monitoring of individual cells over long periods, revealing behaviours that would be masked when looking only at the population level or only at snapshots.
The main microfluidic device developed in this thesis, called the 4-Conditions Microfluidic Chemostat (4CMC), consists of an array of microchemostats exposed to four different environmental conditions. It was validated through a series of experiments with the model organism Bacillus subtilis, which revealed new insights into the effect of spore density on spore germination. The device was also used to elucidate the responsiveness of spores of two non-model soil dwellers, the bacterium Ammoniphilus oxalaticus and the fungus Trichoderma rossicum, both of which are potential biocontrol agents. This research led to new findings on A. oxalaticus spores' response to oxalate, an abundant component of soil, and on the effect of nutrient availability on T. rossicum spores.
The 4CMC was also employed to study the responsiveness of engineered bacteria and yeast communities, revealing behaviours that standard population-level assays had masked, as well as choanoflagellates.
Version
Open Access
Date Issued
2024-10-02
Date Awarded
01/03/2025
License URL
Advisor
Stanley, Claire
Stan, Guy-Bart
Ledesma-Amaro, Rodrigo
Publisher Department
Department of Bioengineering
Publisher Institution
Imperial College London
Qualification Level
Doctoral
Qualification Name
Doctor of Philosophy (PhD)