Microfluidic approaches in microbial ecology

Microfluidic approaches in microbial ecology

2024 | Giovanni Stefano Ugonli, Miaoxiao Wang, Eleonora Secchi, Roberto Pioli, Martin Ackermann, Roman Stocker
Microfluidic approaches have significantly advanced the study of microbial ecology by enabling precise control over environmental conditions at the scale of individual cells and microbial communities. This review highlights how microfluidics has enhanced our understanding of microbial life, from single-cell behaviors to the functioning of multi-cellular communities. Microfluidics allows for the observation and quantification of microbial processes such as growth, motility, and responses to external cues with greater detail than classical techniques. By enabling precise control over nutrient gradients, pH levels, and fluid flow patterns, microfluidics provides a means to study microbial processes in conditions that mimic natural environments. Microfluidics has been particularly useful in studying how bacteria respond to temporal fluctuations in their environment. For example, the Mother Machine, a microfluidic device, allows for the tracking of individual bacterial cells over multiple generations, revealing how phenotypic heterogeneity affects population-level responses. Additionally, microfluidic tools have been developed to expose bacteria to frequent switches between two environmental conditions, enabling the study of how bacteria adapt to periodic fluctuations in nutrient availability or pH. Microfluidics has also enabled the study of microbial navigation in spatially heterogeneous environments. By creating controlled gradients of nutrients and other environmental factors, microfluidic devices allow for the observation of how bacteria move and respond to spatial gradients. These studies have revealed how bacteria use chemotaxis to find optimal nutrient and environmental conditions, and how they navigate through complex environments such as soil, groundwater, and the ocean. Furthermore, microfluidics has been used to study the mechanisms underlying bacterial responses to environmental fluctuations, including the dynamics of gene expression and the transport and accumulation of compounds. By integrating fluorescent labeling with microfluidic technologies, researchers can quantify the behavior of individual cells and track the effects of environmental changes on microbial communities. In addition, microfluidics has contributed to our understanding of cellular memory in changing environments. Environmental conditions can influence a cell's internal state and affect future cellular decision-making. Microfluidic experiments have revealed how cells retain information about past environmental conditions, which can improve their survival and growth in dynamic environments. Overall, microfluidics has provided a powerful platform for studying microbial ecology, enabling the investigation of microbial processes at the single-cell level and offering new insights into how bacteria respond to environmental fluctuations. By integrating microfluidic technologies with fluorescent labeling and high-resolution imaging, researchers can gain a deeper understanding of microbial behavior and the complex interactions that govern microbial communities.Microfluidic approaches have significantly advanced the study of microbial ecology by enabling precise control over environmental conditions at the scale of individual cells and microbial communities. This review highlights how microfluidics has enhanced our understanding of microbial life, from single-cell behaviors to the functioning of multi-cellular communities. Microfluidics allows for the observation and quantification of microbial processes such as growth, motility, and responses to external cues with greater detail than classical techniques. By enabling precise control over nutrient gradients, pH levels, and fluid flow patterns, microfluidics provides a means to study microbial processes in conditions that mimic natural environments. Microfluidics has been particularly useful in studying how bacteria respond to temporal fluctuations in their environment. For example, the Mother Machine, a microfluidic device, allows for the tracking of individual bacterial cells over multiple generations, revealing how phenotypic heterogeneity affects population-level responses. Additionally, microfluidic tools have been developed to expose bacteria to frequent switches between two environmental conditions, enabling the study of how bacteria adapt to periodic fluctuations in nutrient availability or pH. Microfluidics has also enabled the study of microbial navigation in spatially heterogeneous environments. By creating controlled gradients of nutrients and other environmental factors, microfluidic devices allow for the observation of how bacteria move and respond to spatial gradients. These studies have revealed how bacteria use chemotaxis to find optimal nutrient and environmental conditions, and how they navigate through complex environments such as soil, groundwater, and the ocean. Furthermore, microfluidics has been used to study the mechanisms underlying bacterial responses to environmental fluctuations, including the dynamics of gene expression and the transport and accumulation of compounds. By integrating fluorescent labeling with microfluidic technologies, researchers can quantify the behavior of individual cells and track the effects of environmental changes on microbial communities. In addition, microfluidics has contributed to our understanding of cellular memory in changing environments. Environmental conditions can influence a cell's internal state and affect future cellular decision-making. Microfluidic experiments have revealed how cells retain information about past environmental conditions, which can improve their survival and growth in dynamic environments. Overall, microfluidics has provided a powerful platform for studying microbial ecology, enabling the investigation of microbial processes at the single-cell level and offering new insights into how bacteria respond to environmental fluctuations. By integrating microfluidic technologies with fluorescent labeling and high-resolution imaging, researchers can gain a deeper understanding of microbial behavior and the complex interactions that govern microbial communities.
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[slides and audio] Microfluidic approaches in microbial ecology