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ABSTRACT Bacterial motility plays a crucial role in biofilm development, yet the underlying mechanism remains not fully understood. Here, we demonstrate that the flagellum-driven motility ofPseudomonas aeruginosaenhances biofilm formation by altering the orientation of bacterial cells, an effect controlled by shear stress rather than shear rate. By tracking wild-typeP. aeruginosaand its non-motile mutants in a microfluidic channel, we demonstrate that while non-motile cells align with the flow, many motile cells can orient toward the channel sidewalls, enhancing cell surface attachment and increasing biofilm cell density by up to 10-fold. Experiments with varying fluid viscosities further demonstrate that bacterial swimming speed decreases with increasing fluid viscosity, and the cell orientation scales with the shear stress rather than shear rate. Our results provide a quantitative framework to predict the role of motility in the orientation and biofilm development under different flow conditions and viscosities.IMPORTANCEBiofilms are ubiquitous in rivers, water pipes, and medical devices, impacting the environment and human health. While bacterial motility plays a crucial role in biofilm development, a mechanistic understanding remains limited, hindering our ability to predict and control biofilms. Here, we reveal how the motility ofPseudomonas aeruginosa, a common pathogen, influences biofilm formation through systematically controlled microfluidic experiments with confocal and high-speed microscopy. We demonstrate that the orientation of bacterial cells is controlled by shear stress. While non-motile cells primarily align with the flow, many motile cells overcome the fluid shear forces and reorient toward the channel sidewalls, increasing biofilm cell density by up to 10-fold. Our findings provide insights into how bacterial transition from free-swimming to surface-attached states under varying flow conditions, emphasizing the role of cell orientation in biofilm establishment. These results enhance our understanding of bacterial behavior in flow environments, informing strategies for biofilm management and control. 

Abstract Hyporheic exchange leads to the transfer of gases, solutes, and fine particles across the sediment‐water interface, playing a critical role in biogeochemical cycles and pollutant transport in aquatic environments. While in‐channel vegetation has been recognized to enhance hyporheic exchange, the mechanisms remain poorly understood. Here, we investigated how an emergent vegetation canopy impacts hyporheic exchange using refractive index‐matched flume experiments and coupled numerical simulations. Our results show that at the same mean surface flow velocity, vegetation increases the hyporheic exchange velocity by four times compared to the non‐vegetated channel. However, the hyporheic exchange velocity does not increase further with increasing vegetation density. In addition, our results show that the hyporheic exchange velocity scales with the square root of sediment permeability. Our findings provide a predictive framework for hyporheic exchange in vegetated channels with varying vegetation densities and sediment permeabilities and could guide the future design of environmental management and restoration projects using vegetation. 

Abstract In‐channel wood, a critical component of forested rivers, has the capacity to enhance hyporheic flow. This process facilitates the continuous exchange of gases, solutes, and nutrients across the sediment‐water interface, regulating pollutant transport and biogeochemical cycles in rivers. When two wood structures are in close proximity, the hyporheic flows induced by each log can interact, yet such effects remain largely uncharacterized. In this study, we investigated the impact of two in‐line channel‐spanning logs with a vertical gap above the sediment‐water interface on hyporheic flow through laboratory experiments conducted under various conditions. Specifically, we measured water surface profiles, surface flow fields, and hyporheic flow fields around logs with different center‐to‐center distances (). Our results demonstrated that when the center‐to‐center distance between two logs was less than 10 times the log diameter, the wakes of the two logs interfered with each other, resulting in a decrease in both hyporheic flow rates and the difference in water surface elevation. Furthermore, we demonstrated the relationship between the pattern of log‐induced hyporheic flow and the surface flow regime. Our results suggest that the hyporheic flow pattern induced by logs can be inferred from measurements of the surface flow patterns. Our findings will contribute to an improved estimation of hyporheic flow induced by logs distributed along river channels. 

Abstract In‐stream wood structures, such as single logs, river steps, and debris dams, are known to drive hyporheic flow, defined as the flow that goes into the subsurface region and then back to the free‐flowing surface water. The hyporheic flow plays an important role in regulating water quality and biogeochemical cycles in rivers. Here, we investigated the impact of a channel‐spanning porous log jam, representing piles of wood logs, on hyporheic flow through a combination of direct visualization and theories. Specifically, we developed a method using refractive index‐matched sediment to directly visualize the hyporheic flow around and below a porous log jam, formed by piles of cylindrical rods, in a laboratory flume. We tracked the velocity of a fluorescent dye moving through the transparent sediment underneath the log jam. In addition, we measured the water surface profile and the spatially varying flow velocity near the log jam. Our results show that the normalized log jam‐induced hyporheic flux remained smaller than 10% at Froude numbers () below 0.06 and increased by a factor of five with increasing at . We combined the mass and momentum conservation equations of surface flow with Darcy's equation to explain the dependency of the log jam‐induced hyporheic flux on . Further, we observed that at , the water surface dropped noticeably and the turbulent kinetic energy increased immediately on the downstream side of the log jam. These findings will facilitate future quantification of hyporheic flow caused by channel‐spanning porous log jams.