In contexts such as suspension feeding in marine ecologies there is an interplay between brownian motion of nonmotile particles and their advection by flows from swimming microorganisms. As a laboratory realization, we study passive tracers in suspensions of eukaryotic swimmers, the alga Chlamydomonas reinhardtii. While the cells behave ballistically over short intervals, the tracers behave diffusively, with a time-dependent but self-similar probability distribution function of displacements consisting of a gaussian core and robust exponential tails. We emphasize the role of flagellar beating in creating oscillatory flows that exceed brownian motion far from each swimmer.

Bacteria often live in dynamic fluid environments 1-3 and flow can a ect fundamental microbial processes such as nutrient uptake 1,4 and infection 5 . However, little is known about the consequences of the forces and torques associated with fluid flow on bacteria. Through microfluidic experiments, we show that fluid shear produces strong spatial heterogeneity in suspensions of motile bacteria, characterized by up to 70% cell depletion from low-shear regions due to 'trapping' in high-shear regions. Two mathematical models and a scaling analysis accurately capture these observations, including the maximal depletion at mean shear rates of 2.5-10 s −1 , and reveal that trapping by shear originates from the competition between the cell alignment with the flow and the stochasticity in the swimming orientation. We show that this shear-induced trapping directly impacts widespread bacterial behaviours, by hampering chemotaxis and promoting surface attachment. These results suggest that the hydrodynamic environment may directly a ect bacterial fitness and should be carefully considered in the study of microbial processes.We investigated the effect of flow on motile bacteria by tracking them in precisely controlled laminar flows generated in a microfluidic channel (Fig. 1a). To ensure that the dominant velocity gradients occurred in the horizontal observation plane, at the channel mid-depth, we used a microchannel with aspect ratio H /W > 1 (height H = 750 µm; width W = 425 µm). In that plane, the velocity profile, u(y) = U [1 − 4(y/W ) 2 ], where U is the flow velocity at the channel centreline, is parabolic, and, thus, the shear rate S(y) = du/dy = −8yU /W 2 varies linearly with distance y across the channel and is zero at the centreline (Fig. 1b). In this flow, smooth-swimming Bacillus subtilis bacteria swam unperturbed in straight paths (Fig. 1c) when near the centre of the channel, where the local shear rate was small. Conversely, in high-shear-rate regions, trajectories exhibited frequent loops resulting from rotation of the swimming bacteria by the hydrodynamic torque imparted by the local shear (Fig. 1d). The opposite handedness of the loops on either side of the channel centreline reflects the opposite sign of the shear rate (Fig. 1c,d and Supplementary Movie 1). As shown below, these looping trajectories resulted in bacteria becoming trapped in the high-shear region of the channel.At the population scale, this trapping effect resulted in a marked depletion of cells from the central, low-shear region of the flow, and consequently, in an accumulation in the flanking regions of higher shear. When the flow was impulsively started from rest, the initially uniform distribution of cells over the imaging region across the channel width (Fig. 1e) rapidly (5-10 s) evolved into a distribution characterized by considerably fewer cells in the central part of the channel (Fig. 1f-h). The magnitude of the depletion was severe, with local cell concentrations dropping by 70% (Fig. 1h). The absence of depletion in control experime...

The diversity of the morphologies, propulsion mechanisms, flow environments, and behaviors of planktonic microorganisms has long provided inspiration for fluid physicists, with further intrigue provided by the counterintuitive hydrodynamics of their viscous world. Motivation for studying the fluid dynamics of microplankton abounds, as microorganisms support the food web and control the biogeochemistry of most aquatic environments, particularly the oceans. In this review, we discuss the fluid physics governing the locomotion and feeding of individual planktonic microorganisms (≤1 mm). In the past few years, the field has witnessed an increasing number of exciting discoveries, from the visualization of the flow field around individual swimmers to linkages between microhydrodynamic processes and ecosystem dynamics. In other areas, chiefly the ability of microorganisms to take up nutrients and sense hydromechanical signals, our understanding will benefit from reinvigorated interest, and ample opportunities for breakthroughs exist. When it comes to the fluid mechanics of living organisms, there is plenty of room at the bottom. 373 Annu. Rev. Fluid Mech. 2012.44:373-400. Downloaded from www.annualreviews.org by Massachusetts Institute of Technology (MIT) on 02/07/12. For personal use only.

Bacteria swim by rotating rigid helical flagella and periodically reorienting to follow environmental cues 1,2 . Despite the crucial role of reorientations, their underlying mechanism has remained unknown for most uni-flagellated bacteria 3,4 . Here, we report that uni-flagellated bacteria turn by exploiting a finely tuned buckling instability of their hook, the 100-nm-long structure at the base of their flagellar filament 5 . Combining high-speed video microscopy and mechanical stability theory, we demonstrate that reorientations occur 10 ms after the onset of forward swimming, when the hook undergoes compression, and that the associated hydrodynamic load triggers the buckling of the hook. Reducing the load on the hook below the buckling threshold by decreasing the swimming speed results in the suppression of reorientations, consistent with the critical nature of buckling. The mechanism of turning by buckling represents one of the smallest examples in nature of a biological function stemming from controlled mechanical failure 6 and reveals a new role for flexibility in biological materials, which may inspire new microrobotic solutions in medicine and engineering 7 .Flexibility is woven into every facet of living materials. At the cellular level, flexibility allows red blood cells to squeeze through capillaries 8 and DNA to stretch and twist to compensate for variability in binding site length 9 . At the organismal level, flexibility enhances structural performance, for example by enabling animal bones and plant branches to absorb mechanical energy 10 . Flexibility also underpins a host of dynamic life functions, including locomotion, reproduction and predation, by enabling the storage and swift release of elastic energy, a mechanism used by jumping froghoppers to escape predators 11 , by plants to catapult seeds for dispersal 12 , and by aquatic invertebrates to suck in prey 13 . An extreme consequence of flexibility is the occurrence of mechanical instabilities, such as buckling and fluttering, which in engineered systems are synonymous with failure 14 , but in natural systems can serve functional purpose. The biomechanical repertoire of organisms includes mechanical instabilities over a wide range of timescales, from the millisecond snap-buckling instabilities that allow Venus flytraps 15 and humming birds 16 to capture insects to the gradual buckling responsible for the wavy edges of leaves and flowers 17 .Flexible appendages are widely used by organisms for locomotion in fluids, from the flapping of bird and bat wings 18 , to the actuation of fish fins 19 , to the bending of sperm flagella 20 . Flexibility also plays a subtle role in the locomotion of bacteria with multiple flagella (peritrichous), such as Escherichia coli, which bundles its flagella together for propulsion (a run 1 ) by exploiting the compliance of the flagellum's base 21,22 . When one or more flagella leave the bundle following a change in the direction of rotation of their motor, the torque resulting from the unbundling, or from the asso...

We present the first time-resolved measurements of the oscillatory velocity field induced by swimming unicellular microorganisms. Confinement of the green alga C. reinhardtii in stabilized thin liquid films allows simultaneous tracking of cells and tracer particles. The measured velocity field reveals complex time-dependent flow structures, and scales inversely with distance. The instantaneous mechanical power generated by the cells is measured from the velocity fields and peaks at 15 fW. The dissipation per cycle is more than 4 times what steady swimming would require.

Fluid mixing in active suspensions of microorganisms is important to ecological phenomena and presents a fascinating stochastic process. We investigate the mixing produced by swimming unicellular algal cells (Chlamydomonas) in quasi-two-dimensional liquid films by simultaneously tracking the motion of the cells and that of microscopic passive tracer particles advected by the fluid. The reduced spatial dimension of the system leads to long-range flows and a surprisingly strong dependence of tracer transport on the concentration of swimmers, which is explored over a wide range. The mean square displacements are well described by a stochastic Langevin model, which is used to parameterize the mixing. The effective diffusion coefficient D grows rapidly with the swimmer concentration Φ as D ∼ Φ 3∕2 , as a result of the increasing frequency of tracer-swimmer interactions and the long-range hydrodynamic disturbances created by the swimmers. Conditional sampling of the tracer data based on the instantaneous swimmer position shows that the rapid growth of the diffusivity enhancement with concentration must be due to particle interactions with multiple swimmers simultaneously. Finally, the anomalous probability distributions of tracer displacements become Gaussian at high concentration, but manifest strong power-law tails at low concentration, while the tracer displacements always grow diffusively in time.biofluid dynamics | low Reynolds number | flagella

The exchange of nutrients and dissolved gasses between corals and their environment is a critical determinant of the growth of coral colonies and the productivity of coral reefs. To date, this exchange has been assumed to be limited by molecular diffusion through an unstirred boundary layer extending 1-2 mm from the coral surface, with corals relying solely on external flow to overcome this limitation. Here, we present direct microscopic evidence that, instead, corals can actively enhance mass transport through strong vortical flows driven by motile epidermal cilia covering their entire surface. Ciliary beating produces quasi-steady arrays of counterrotating vortices that vigorously stir a layer of water extending up to 2 mm from the coral surface. We show that, under low ambient flow velocities, these vortices, rather than molecular diffusion, control the exchange of nutrients and oxygen between the coral and its environment, enhancing mass transfer rates by up to 400%. This ability of corals to stir their boundary layer changes the way that we perceive the microenvironment of coral surfaces, revealing an active mechanism complementing the passive enhancement of transport by ambient flow. These findings extend our understanding of mass transport processes in reef corals and may shed new light on the evolutionary success of corals and coral reefs.coral microenvironment | coral reef evolution | diffusion boundary layer | microfluidics | biological fluid mechanics

Viscoelastic flows transition from steady to time-dependent, chaotic dynamics under critical flow conditions, but the implications of geometric disorder for flow stability in these systems are unknown. Utilizing microfluidics, we flow a viscoelastic fluid through arrays of cylindrical pillars, which are perturbed from a hexagonal lattice with various degrees of geometric disorder. Small disorder, corresponding to ∼ 10% of the lattice constant, delays the transition to higher flow speeds, while larger disorders exhibit near-complete suppression of chaotic velocity fluctuations. We show that the mechanism facilitating flow stability at high disorder is rooted in a shift from extension-dominated to shear-dominated flow type with increasing disorder.