Patterns of bacterial motility in microfluidics-confining environments

Understanding the motility behavior of bacteria in confining microenvironments, in which they search for available physical space and move in response to stimuli, is important for environmental, food industry, and biomedical applications. We studied the motility of five bacterial species with various sizes and flagellar architectures (Vibrio natriegens, Magnetococcus marinus, Pseudomonas putida, Vibrio fischeri, and Escherichia coli) in microfluidic environments presenting various levels of confinement and geometrical complexity, in the absence of external flow and concentration gradients. When the confinement is moderate, such as in quasi-open spaces with only one limiting wall, and in wide channels, the motility behavior of bacteria with complex flagellar architectures approximately follows the hydrodynamics-based predictions developed for simple monotrichous bacteria. Specifically, V. natriegens and V. fischeri moved parallel to the wall and P. putida and E. coli presented a stable movement parallel to the wall but with incidental wall escape events, while M. marinus exhibited frequent flipping between wall accumulator and wall escaper regimes. Conversely, in tighter confining environments, the motility is governed by the steric interactions between bacteria and the surrounding walls. In mesoscale regions, where the impacts of hydrodynamics and steric interactions overlap, these mechanisms can either push bacteria in the same directions in linear channels, leading to smooth bacterial movement, or they could be oppositional (e.g., in mesoscale-sized meandered channels), leading to chaotic movement and subsequent bacterial trapping. The study provides a methodological template for the design of microfluidic devices for single-cell genomic screening, bacterial entrapment for diagnostics, or biocomputation.

Many motile bacteria live in confining microenvironments (e.g., animal or plant tissue, soil, waste, granulated, and porous materials) and consequently are important to many applications like health infectious diseases (1, 2), pharmaceuticals (3), and nutrition (4)], agriculture veterinary (5) and crops (6)], environmental science photosynthesis (7), biodegradation (8), and bioremediation (9)], and industrial activities mining (10) and biofouling (11)]. Bacterial motility is essential in the search for available physical space as well as for enabling bacterial taxis in response to external stimuli, such as temperature (12), chemical gradients (13, 14), mechanical cues (15), or magnetic fields (16).To thrive in environments with diverse geometrical and physical characteristics, from open spaces to constraining environments, motile bacteria have evolved a multitude of propelling mechanisms (17), with flagellum-driven being the most common (18, 19). Flagellum-based machinery features various numbers of flagella (20) and designs: monotrichous, lophotrichous, amphitrichous, or peritrichous. The mechanics of this machinery, coupled with cell morphology (21) (e.g., coccus, rod-like, or curved) translates into several motility modes (e.g., turn angle, run-and-tumble, or run-and-flick) (22), and various motility behaviors (e.g., swimming, tumbling, and swarming) (17, 23). Environmental factors (24, 25) (e.g., chemical composition, viscosity, temperature, pH, and the chemistry and the roughness of adjacent surfaces) also influence bacterial motility.“Pure” bacterial motility, unbiased by chemotaxis or fluid flow, was reported near simple flat surfaces (26, 27) and in channels (28–30). Simulations of model bacteria in analogous conditions were also undertaken (31–37), but owing to the complexity of bacterial mechanics (38), modeling from first principles did not provide sufficient understanding to accurately predict movement patterns of different species in complex, confined environments. Consequently, studies of the effects of bacterial geometry in confined geometries were limited to models of simple, monotrichous bacteria with an assumed rigid flagellum (32, 39).Microfluidic devices (40, 41) are commonly used for the manipulation of individual or small populations of cells in micrometer-sized channels for medical diagnostics (42), drug screening (43), cell separation (44, 45), detection and sorting (46), and single-cell genomics (47). While microfluidic structures are used for the study of the motility of mammalian cells (48, 49), and microorganisms e.g., fungi (50, 51), algae (52), or bacteria (29, 53–56)], these studies typically focus on a single species.To make progress toward a more general understanding of the motility of individual bacterial cells in confining microenvironments, as well as to assess the extent to which the behavior of bacteria with complex architectures can be assimilated with that of the more predictable monotrichous bacteria, the present work investigated the movement of five species (i.e., Vibrio natriegens, Magnetococcus marinus, Pseudomonas putida, Vibrio fischeri, and Escherichia coli) in microfluidic geometries with various levels of confinement and geometrical complexity.