Bacteria in Fluid Flow

Abstract

Bacteria thrive in environments rich in fluid flow, such as the gastrointestinal tract, bloodstream, aquatic systems, and the urinary tract. Despite the importance of flow, how flow affects bacterial life is underappreciated. In recent years, the combination of approaches from biology, physics, and engineering has led to a deeper understanding of how bacteria interact with flow. Here, we highlight the wide range of bacterial responses to flow, including changes in surface adhesion, motility, surface colonization, quorum sensing, virulence factor production, and gene expression. To emphasize the diversity of flow responses, we focus our review on how flow affects four ecologically distinct bacterial species: Escherichia coli, Staphylococcus aureus, Caulobacter crescentus, and Pseudomonas aeruginosa. Additionally, we present experimental approaches to precisely study bacteria in flow, discuss how only some flow responses are triggered by shear force, and provide perspective on flow-sensitive bacterial signaling.

Keywords: adhesion; bacteria; colonization; fluid flow; gene expression; mechanobiology; mechanosensing; motility; quorum sensing; virulence.

FIG 1

Implementation of microfluidics to study bacteria in flow. (A) A syringe pump can modulate the flow rate of a microfluidic system. Here, we show an example syringe pump set to a flow rate. The syringe pump pushes a syringe to inject medium through tubing into a microfluidic device. (B) A microfluidic device is loaded onto the stage of an inverted fluorescence microscope for imaging. Medium exits the microfluidic device through tubing that leads to a waste container. (C) Enlarged depiction of a microfluidic chip on the microscope stage. Black arrows indicate the movement of fluid through tubing into and out of the microfluidic device. (D) Enlarged schematic showing the dimensions of a simple microfluidic device. Microfluidic devices can be different sizes. Here, we illustrate an example of a microfluidic device containing one channel. The darker gray shape depicts polydimethylsiloxane (PDMS), while the lighter gray shape depicts a glass coverslip. (E) Equations for shear rate, shear stress, and shear force. Shear rate is proportional to flow rate and inversely proportional to channel width and the square of channel height. Shear stress is the product of shear rate and media viscosity. Shear force is conceptually similar to shear stress but also depends on cell size.

FIG 2

Bacterial surface adhesion in flow. (A) Escherichia coli in flow adhered to a mannose-coated surface using type I fimbriae. The small red boxes are magnified in the detailed illustrations below. The figure depicts the inner membrane (IM), peptidoglycan (PG), and outer membrane (OM) with type I fimbriae anchored to the outer membrane. The protein FimH is attached to the end of the type I fimbriae via its pilin domain (shown in teal) and binds to mannose via its lectin-binding domain (shown in blue). In conditions with high shear flow, the FimH exhibits catch bond behavior and increases binding strength to mannose. (B) Staphylococcus aureus in flow adhered to a fibrinogen-coated surface using clumping factor A (ClfA) (shown in purple). ClfA is anchored to the peptidoglycan (PG) cell wall. ClfA binds fibrinogen using a “dock-lock-latch” mechanism via its N2 and N3 domains. (C) Caulobacter crescentus in flow adhered a glass surface using a polysaccharide called the holdfast (shown in green) on the end of its polar stalk appendage. The holdfast matrix consists of glucose, mannose, N-acetylglucosamine, and xylose. (D) Pseudomonas aeruginosa in flow adhered to a glass surface using type IV pili (shown in blue). Type IV pili are assembled from PilA monomers, which are added by the extension motor PilB and removed by the retraction motor PilT. Addition of PilA monomers leads to extension of the type IV pilus, while removal of PilA monomers leads to retraction of the type IV pilus.

FIG 3

How flow affects major bacterial paradigms. (A) Pseudomonas aeruginosa cells use extension and retraction of type IV pili (shown in blue) to move on surfaces via twitching motility. In conditions without flow, twitching motility does not typically proceed in a directed manner. In flow, cells are reoriented along the axis of flow, which leads to directed movement against the direction of flow. (B) Caulobacter crescentus cells divide asymmetrically. Without flow, mother cells typically remain attached to a surface via their holdfasts (green circles), and daughter cells (shown in orange) leave the surface via flagellar motility. In flow, mother cells tip over, daughter cells are in close proximity with the surface, and the frequency of daughter cell surface attachment increases. (C) Quorum sensing involves the release and capture of autoinducers to regulate gene expression and behavior. Staphylococcus aureus uses peptide-based autoinducers (shown as red triangles) for quorum sensing. In conditions without flow, cells sense autoinducer concentration as a proxy for cell density. However, flow removes autoinducers and creates a situation in which autoinducer concentration does not accurately correspond to cell density.

FIG 4

Bacterial flow-sensitive gene expression. (A) Model of flow-sensitive gene expression in enterohemorrhagic Escherichia coli. Locus of enterocyte effacement (LEE) genes are induced by flow. While it is thought that shear force triggers a release of the protein GrlA (shown in red) from the inner membrane, the mechanism underlying this release is unknown. GrlA is an activator that promotes transcription of LEE genes by RNA polymerase (RNAP). (B) Model of flow-sensitive gene expression in Pseudomonas aeruginosa strain PAO1. Expression of the adhesin-encoding gene cdrA was shown to be induced by low levels of flow. While it is thought that shear force triggers the intracellular accumulation of the secondary messenger cyclic di-GMP, the mechanism underlying this accumulation is unknown. FleQ (shown in purple) is a cyclic di-GMP-responsive repressor that blocks transcription of cdrA by RNA polymerase (RNAP). (C) Model of flow-sensitive gene expression in Pseudomonas aeruginosa strain PA14. Expression of the froABCD operon is induced by shear rate. While flow-sensitive fro expression requires the alternative sigma factor FroR (shown in orange) and anti-sigma factor FroI (shown in blue), the mechanism of how flow triggers signaling is unknown.