Rapid Chemotactic Response Enables Marine Bacteria to Exploit Ephemeral Microscale Nutrient Patches

Proceedings of the National Academy of Sciences of the United States of America. Mar, 2008  |  Pubmed ID: 18337491

Because ocean water is typically resource-poor, bacteria may gain significant growth advantages if they can exploit the ephemeral nutrient patches originating from numerous, small sources. Although this interaction has been proposed to enhance biogeochemical transformation rates in the ocean, it remains questionable whether bacteria are able to efficiently use patches before physical mechanisms dissipate them. Here we show that the rapid chemotactic response of the marine bacterium Pseudoalteromonas haloplanktis substantially enhances its ability to exploit nutrient patches before they dissipate. We investigated two types of patches important in the ocean: nutrient pulses and nutrient plumes, generated for example from lysed algae and sinking organic particles, respectively. We used microfluidic devices to create patches with environmentally realistic dimensions and dynamics. The accumulation of P. haloplanktis in response to a nutrient pulse led to formation of bacterial hot spots within tens of seconds, resulting in a 10-fold higher nutrient exposure for the fastest 20% of the population compared with nonmotile cells. Moreover, the chemotactic response of P. haloplanktis was >10 times faster than the classic chemotaxis model Escherichia coli, leading to twice the nutrient exposure. We demonstrate that such rapid response allows P. haloplanktis to colonize nutrient plumes for realistic particle sinking speeds, with up to a 4-fold nutrient exposure compared with nonmotile cells. These results suggest that chemotactic swimming strategies of marine bacteria in patchy nutrient seascapes exert strong influence on carbon turnover rates by triggering the formation of microscale hot spots of bacterial productivity.

Experimental Verification of the Behavioral Foundation of Bacterial Transport Parameters Using Microfluidics

Biophysical Journal. Nov, 2008  |  Pubmed ID: 18658218

We present novel microfluidic experiments to quantify population-scale transport parameters (chemotactic sensitivity chi(0) and random motility mu) of a population of bacteria. Previously, transport parameters have been derived theoretically from single-cell swimming behavior using probabilistic models, yet the mechanistic foundations of this upscaling process have not been verified experimentally. We designed a microfluidic capillary assay to generate and accurately measure gradients of chemoattractant (alpha-methylaspartate) while simultaneously capturing the swimming trajectories of individual Escherichia coli bacteria using videomicroscopy and cell tracking. By measuring swimming speed and bias in the swimming direction of single cells for a range of chemoattractant concentrations and concentration gradients, we directly computed the chemotactic velocity VC and the associated chemotactic sensitivity chi(0). We then show how mu can also be readily determined using microfluidics but that a population-scale microfluidic approach is experimentally more convenient than a single-cell analysis in this case. Measured values of both chi(0) [(12.4 +/- 2.0) x 10(-4) cm(2) s(-1)] and mu [(3.3 +/- 0.8) x 10(-6) cm(2) s(-1)] are comparable to literature results. This microscale approach to bacterial chemotaxis lends experimental support to theoretical derivations of population-scale transport parameters from single-cell behavior. Furthermore, this study shows that microfluidic platforms can go beyond traditional chemotaxis assays and enable the quantification of bacterial transport parameters.

Disruption of Vertical Motility by Shear Triggers Formation of Thin Phytoplankton Layers

Science (New York, N.Y.). Feb, 2009  |  Pubmed ID: 19229037

Thin layers of phytoplankton are important hotspots of ecological activity that are found in the coastal ocean, meters beneath the surface, and contain cell concentrations up to two orders of magnitude above ambient concentrations. Current interpretations of their formation favor abiotic processes, yet many phytoplankton species found in these layers are motile. We demonstrated that layers formed when the vertical migration of phytoplankton was disrupted by hydrodynamic shear. This mechanism, which we call gyrotactic trapping, can be responsible for the thin layers of phytoplankton commonly observed in the ocean. These results reveal that the coupling between active microorganism motility and ambient fluid motion can shape the macroscopic features of the marine ecological landscape.

Separation of Microscale Chiral Objects by Shear Flow

Physical Review Letters. Apr, 2009  |  Pubmed ID: 19522552

We show that plane parabolic flow in a microfluidic channel causes nonmotile, helically shaped bacteria to drift perpendicular to the shear plane. Net drift results from the preferential alignment of helices with streamlines, with a direction that depends on the chirality of the helix and the sign of the shear rate. The drift is in good agreement with a model based on resistive force theory, and separation is efficient (>80%) and fast (<2 s). We estimate the effect of Brownian rotational diffusion on chiral separation and show how this method can be extended to separate chiral molecules.

Microbiology. Tumbling for Stealth?

Science (New York, N.Y.). Jul, 2009  |  Pubmed ID: 19628846

Chemoattraction to Dimethylsulfoniopropionate Throughout the Marine Microbial Food Web

Science (New York, N.Y.). Jul, 2010  |  Pubmed ID: 20647471

Phytoplankton-produced dimethylsulfoniopropionate (DMSP) provides underwater and atmospheric foraging cues for several species of marine invertebrates, fish, birds, and mammals. However, its role in the chemical ecology of marine planktonic microbes is largely unknown, and there is evidence for contradictory functions. By using microfluidics and image analysis of swimming behavior, we observed attraction toward microscale pulses of DMSP and related compounds among several motile strains of phytoplankton, heterotrophic bacteria, and bacterivore and herbivore microzooplankton. Because microbial DMSP cycling is the main natural source of cloud-forming sulfur aerosols, our results highlight how adaptations to microscale chemical seascapes shape planktonic food webs, while potentially influencing climate at the global scale.

Bacterial Chemotaxis in Linear and Nonlinear Steady Microfluidic Gradients

Nano Letters. Sep, 2010  |  Pubmed ID: 20669946

Diffusion-based microfluidic devices can generate steady, arbitrarily shaped chemical gradients without requiring fluid flow and are ideal for studying chemotaxis of free-swimming cells such as bacteria. However, if microfluidic gradient generators are to be used to systematically study bacterial chemotaxis, it is critical to evaluate their performance with actual quantitative chemotaxis tests. We characterize and compare three diffusion-based gradient generators by confocal microscopy and numerical simulations, select an optimal design and apply it to chemotaxis experiments with Escherichia coli in both linear and nonlinear gradients. Comparison of the observed cell distribution along the gradients with predictions from an established mathematical model shows very good agreement, providing the first quantification of chemotaxis of free-swimming cells in steady nonlinear microfluidic gradients and opening the door to bacterial chemotaxis studies in gradients of arbitrary shape.

Filtration of Submicrometer Particles by Pelagic Tunicates

Proceedings of the National Academy of Sciences of the United States of America. Aug, 2010  |  Pubmed ID: 20696887

Salps are common in oceanic waters and have higher per-individual filtration rates than any other zooplankton filter feeder. Although salps are centimeters in length, feeding via particle capture occurs on a fine, mucous mesh (fiber diameter d approximately 0.1 microm) at low velocity (U = 1.6 +/- 0.6 cmxs(-1), mean +/- SD) and is thus a low Reynolds-number (Re approximately 10(-3)) process. In contrast to the current view that particle encounter is dictated by simple sieving of particles larger than the mesh spacing, a low-Re mathematical model of encounter rates by the salp feeding apparatus for realistic oceanic particle-size distributions shows that submicron particles, due to their higher abundances, are encountered at higher rates (particles per time) than larger particles. Data from feeding experiments with 0.5-, 1-, and 3-microm diameter polystyrene spheres corroborate these findings. Although particles larger than 1 microm (e.g., flagellates, small diatoms) represent a larger carbon pool, smaller particles in the 0.1- to 1-microm range (e.g., bacteria, Prochlorococcus) may be more quickly digestible because they present more surface area, and we find that particles smaller than the mesh size (1.4 microm) can fully satisfy salp energetic needs. Furthermore, by packaging submicrometer particles into rapidly sinking fecal pellets, pelagic tunicates can substantially change particle-size spectra and increase downward fluxes in the ocean.

Microfluidics for Bacterial Chemotaxis

Integrative Biology : Quantitative Biosciences from Nano to Macro. Nov, 2010  |  Pubmed ID: 20967322

Microfluidics is revolutionizing the way we study the motile behavior of cells, by enabling observations at high spatial and temporal resolution in carefully controlled microenvironments. An important class of such behavior is bacterial chemotaxis, which plays a fundamental role in a broad range of processes, including disease pathogenesis, biofilm formation, bioremediation, and even carbon cycling in the ocean. In biophysical research, bacterial chemotaxis represents a powerful model system to understand how cells and organisms sense and respond to gradients. Using microfluidics to study chemotaxis of free-swimming bacteria presents experimental challenges that are distinct from those arising in chemotaxis studies of surface-adherent cells. Recently, these challenges have been met by the development of advanced microdevices, able to generate flow-free, steady gradients of arbitrary shape. Much attention to date has been focused on tool development. Yet, we are now at an exciting turning point where science begins to balance technology. Indeed, recent microfluidic studies provided new insights on both the mechanisms governing bacterial gradient sensing (e.g. tuning of response sensitivity, discrimination between conflicting gradients) and the large-scale consequences of chemotaxis (e.g. in the oceans). Here we outline the principles underlying recently proposed gradient generators for bacterial chemotaxis, illustrate the advantage of the microfluidic approach through selected examples, and identify a broader set of scientific questions that may now be addressed with this rapidly developing technology. The latest generation of microfluidic gradient generators, in particular, holds appeal for both biophysicists seeking to unravel the fundamental mechanisms of bacterial chemotaxis, and ecologists wishing to model chemotaxis in realistic environments. Time is ripe for a deeper integration between technology and biology in fully bringing to bear microfluidics on studies of this fascinating microbial behavior.

How Cats Lap: Water Uptake by Felis Catus

Science (New York, N.Y.). Nov, 2010  |  Pubmed ID: 21071630

Animals have developed a range of drinking strategies depending on physiological and environmental constraints. Vertebrates with incomplete cheeks use their tongue to drink; the most common example is the lapping of cats and dogs. We show that the domestic cat (Felis catus) laps by a subtle mechanism based on water adhesion to the dorsal side of the tongue. A combined experimental and theoretical analysis reveals that Felis catus exploits fluid inertia to defeat gravity and pull liquid into the mouth. This competition between inertia and gravity sets the lapping frequency and yields a prediction for the dependence of frequency on animal mass. Measurements of lapping frequency across the family Felidae support this prediction, which suggests that the lapping mechanism is conserved among felines.

Diffusion-limited Retention of Porous Particles at Density Interfaces

Proceedings of the National Academy of Sciences of the United States of America. Dec, 2010  |  Pubmed ID: 21135242

Downward carbon flux in the ocean is largely governed by particle settling. Most marine particles settle at low Reynolds numbers and are highly porous, yet the fluid dynamics of this regime have remained unexplored. We present results of an experimental investigation of porous particles settling through a density interface at Reynolds numbers between 0.1 and 1. We tracked 100 to 500 μm hydrogel spheres with 95.5% porosity and negligible permeability. We found that a small negative initial excess density relative to the lower (denser) fluid layer, a common scenario in the ocean, results in long retention times of particles at the interface. We hypothesized that the retention time was determined by the diffusive exchange of the stratifying agent between interstitial and ambient fluid, which increases excess density of particles that have stalled at the interface, enabling their settling to resume. This hypothesis was confirmed by observations, which revealed a quadratic dependence of retention time on particle size, consistent with diffusive exchange. These results demonstrate that porosity can control retention times and therefore accumulation of particles at density interfaces, a mechanism that could underpin the formation of particle layers frequently observed at pycnoclines in the ocean. We estimate retention times of 3 min to 3.3 d for the characteristic size range of marine particles. This enhancement in retention time can affect carbon transformation through increased microbial colonization and utilization of particles and release of dissolved organics. The observed size dependence of the retention time could further contribute to improve quantifications of vertical carbon flux.

Reverse and Flick: Hybrid Locomotion in Bacteria

Proceedings of the National Academy of Sciences of the United States of America. Feb, 2011  |  Pubmed ID: 21289282

Microbial Alignment in Flow Changes Ocean Light Climate

Proceedings of the National Academy of Sciences of the United States of America. Mar, 2011  |  Pubmed ID: 21368125

The growth of microbial cultures in the laboratory often is assessed informally with a quick flick of the wrist: dense suspensions of microorganisms produce translucent "swirls" when agitated. Here, we rationalize the mechanism behind this phenomenon and show that the same process may affect the propagation of light through the upper ocean. Analogous to the shaken test tubes, the ocean can be characterized by intense fluid motion and abundant microorganisms. We demonstrate that the swirl patterns arise when elongated microorganisms align preferentially in the direction of fluid flow and alter light scattering. Using a combination of experiments and mathematical modeling, we find that this phenomenon can be recurrent under typical marine conditions. Moderate shear rates (0.1 s(-1)) can increase optical backscattering of natural microbial assemblages by more than 20%, and even small shear rates (0.001 s(-1)) can increase backscattering from blooms of large phytoplankton by more than 30%. These results imply that fluid flow, currently neglected in models of marine optics, may exert an important control on light propagation, influencing rates of global carbon fixation and how we estimate these rates via remote sensing.

The Ciliate Paramecium Shows Higher Motility in Non-uniform Chemical Landscapes

PloS One. 2011  |  Pubmed ID: 21494596

We study the motility behavior of the unicellular protozoan Paramecium tetraurelia in a microfluidic device that can be prepared with a landscape of attracting or repelling chemicals. We investigate the spatial distribution of the positions of the individuals at different time points with methods from spatial statistics and Poisson random point fields. This makes quantitative the informal notion of "uniform distribution" (or lack thereof). Our device is characterized by the absence of large systematic biases due to gravitation and fluid flow. It has the potential to be applied to the study of other aquatic chemosensitive organisms as well. This may result in better diagnostic devices for environmental pollutants.

On the Water Lapping of Felines and the Water Running of Lizards: A Unifying Physical Perspective

Communicative & Integrative Biology. Mar, 2011  |  Pubmed ID: 21655444

We consider two biological phenomena taking place at the air-water interface: the water lapping of felines and the water running of lizards. Although seemingly disparate motions, we show that they are intimately linked by their underlying hydrodynamics and belong to a broader class of processes called Froude mechanisms. We describe how both felines and lizards exploit inertia to defeat gravity, and discuss water lapping and water running in the broader context of water exit and water entry, respectively.

Gyrotaxis in a Steady Vortical Flow

Physical Review Letters. Jun, 2011  |  Pubmed ID: 21770545

We show that gyrotactic motility within a steady vortical flow leads to tightly clustered aggregations of microorganisms. Two dimensionless numbers, characterizing the relative swimming speed and stability against overturning by vorticity, govern the coupling between motility and flow. Exploration of parameter space reveals a striking array of patchiness regimes. Aggregations are found to form within a few overturning time scales, suggesting that vortical flows might be capable of efficiently separating species with different motility characteristics.

Response Rescaling in Bacterial Chemotaxis

Proceedings of the National Academy of Sciences of the United States of America. Aug, 2011  |  Pubmed ID: 21808031

Sensory systems rescale their response sensitivity upon adaptation according to simple strategies that recur in processes as diverse as single-cell signaling, neural network responses, and whole-organism perception. Here, we study response rescaling in Escherichia coli chemotaxis, where adaptation dynamically tunes the cells' motile response during searches for nutrients. Using in vivo fluorescence resonance energy transfer (FRET) measurements on immobilized cells, we demonstrate that the design of this prokaryotic signaling network follows the fold-change detection (FCD) strategy, responding faithfully to the shape of the input profile irrespective of its absolute intensity. Using a microfluidics-based assay for free swimming cells, we confirm intensity-independent gradient responses at the behavioral level. By theoretical analysis, we identify a set of sufficient conditions for FCD in E. coli chemotaxis, which leads to the prediction that the adaptation timescale is invariant with respect to the background input level. Additional FRET experiments confirm that the adaptation timescale is invariant over an ∼10,000-fold range of background concentrations. These observations in a highly optimized bacterial system support the concept that FCD represents a robust sensing strategy for spatial searches. To our knowledge, these experiments provide a unique demonstration of FCD in any biological sensory system.

Systematic Spatial Bias in DNA Microarray Hybridization is Caused by Probe Spot Position-dependent Variability in Lateral Diffusion

PloS One. 2011  |  Pubmed ID: 21858215

The hybridization of nucleic acid targets with surface-immobilized probes is a widely used assay for the parallel detection of multiple targets in medical and biological research. Despite its widespread application, DNA microarray technology still suffers from several biases and lack of reproducibility, stemming in part from an incomplete understanding of the processes governing surface hybridization. In particular, non-random spatial variations within individual microarray hybridizations are often observed, but the mechanisms underpinning this positional bias remain incompletely explained.

Microfluidic Characterization and Continuous Separation of Cells and Particles Using Conducting Poly(dimethyl Siloxane) Electrode Induced Alternating Current-dielectrophoresis

Analytical Chemistry. Dec, 2011  |  Pubmed ID: 22035423

This paper presents a poly(dimethyl siloxane) (PDMS) polymer microfluidic device using alternating current (ac) dielectrophoresis (DEP) for separating live cells from interfering particles of similar sizes by their polarizabilities under continuous flow and for characterizing DEP behaviors of cells in stagnant flow. The ac-DEP force is generated by three-dimensional (3D) conducting PDMS composite electrodes fabricated on a sidewall of the device main channel. Such 3D PDMS composite electrodes are made by dispersing microsized silver (Ag) fillers into PDMS gel. The sidewall AgPDMS electrodes can generate a 3D electric field that uniformly distributes throughout the channel height and varies along the channel lateral direction, thereby producing stronger lateral DEP effects over the entire channel. This allows not only easy observation of cell/particle lateral motion but also using the lateral DEP force for manipulation of cells/particles. The former feature is used to characterize the frequency-dependent DEP behaviors of Saccharomyces cerevisiae (yeast) and Escherichia coli (bacteria). The latter is utilized for continuous separation of live yeast and bacterial cells from similar-size latex particles as well as live yeast cells from dead yeast cells. The separation efficiency of 97% is achieved in all cases. The demonstration of these functions shows promising applications of the microfluidic device.