Differential Dynamic Microscopy: a High-Throughput Method for Characterizing the Motility of Microorganism
Vincent A. Martinez, Rut Besseling, Ottavio A. Croze, Julien Tailleur, Mathias Reufer, Jana Schwarz-Linek, Laurence G. Wilson, Martin A. Bees, Wilson C. K. Poon
We present a fast, high-throughput method for characterizing the motility of microorganisms in 3D based on standard imaging microscopy. Instead of tracking individual cells, we analyse the spatio-temporal fluctuations of the intensity in the sample from time-lapse images and obtain the intermediate scattering function (ISF) of the system. We demonstrate our method on two different types of microorganisms: bacteria, both smooth swimming (run only) and wild type (run and tumble) Escherichia coli, and the bi-flagellate alga Chlamydomonas reinhardtii. We validate the methodology using computer simulations and particle tracking. From the ISF, we are able to extract (i) for E. coli: the swimming speed distribution, the fraction of motile cells and the diffusivity, and (ii) for C. reinhardtii: the swimming speed distribution, the amplitude and frequency of the oscillatory dynamics. In both cases, the motility parameters are averaged over \approx 10^4 cells and obtained in a few minutes.
The motility of microorganisms in liquid media is an important issue in active matter and it is not yet fully understood. Previous theoretical approaches dealing with the microscopic description of microbial movement have modeled the propelling force exerted by the organism as a Gaussian white noise term in the equation of motion. We present experimental results for ciliates of the genus Colpidium, which do not agree with the Gaussian white noise hypothesis. We propose a new stochastic model that goes beyond such assumption and displays good agreement with the experimental statistics of motion…
Marine microorganisms often reach high swimming speeds, either to take advantage of evanescent nutrient patches or to beat Brownian forces. Since this implies that a sizable part of their energetic budget must be allocated to motion, it is reasonable to assume that some fast-swimming microorganisms may increase their nutrient intake by increasing their speed v. We formulate a model to investigate this hypothesis and its consequences, finding the steady state solutions and analyzing their stability. Surprisingly, we find that even modest increases in nutrient absorption may lead to a significan…
Cell motility in viscous fluids is ubiquitous and affects many biological processes, including reproduction, infection, and the marine life ecosystem. Here we review the biophysical and mechanical principles of locomotion at the small scales relevant to cell swimming (tens of microns and below). The focus is on the fundamental flow physics phenomena occurring in this inertia-less realm, and the emphasis is on the simple physical picture. We review the basic properties of flows at low Reynolds number, paying special attention to aspects most relevant for swimming, such as resistance matrices fo…
Microorganisms, such as bacteria and microalgae, often live in habitats consisting of a liquid phase and a plethora of interfaces. The precise ways in which these motile microbes behave in their confined environment remain unclear. Using experiments, Brownian dynamics simulations, and analytical theory, we study the motility of a single Chlamydomonas microalga in an isolated microhabitat with controlled geometric properties. We demonstrate how the geometry of the habitat controls the cell's navigation in confinement. The probability of finding the cell swimming near the boundary scales linearl…
The natural habitats of microorganisms in the human microbiome and ocean and soil ecosystems are full of colloids and macromolecules, which impart non-Newtonian flow properties drastically affecting the locomotion of swimming microorganisms. Although the low-Reynolds-number hydrodynamics of the swimming of flagellated bacteria in simple Newtonian fluids has been well developed, our understanding of bacterial motility in complex non-Newtonian fluids is still primitive. Even after six decades of research, fundamental questions about the nature and origin of bacterial motility enhancement in poly…
One approach to quantifying biological diversity consists of characterizing the statistical distribution of specific properties of a taxonomic group or habitat. Microorganisms living in fluid environments, and for whom motility is key, exploit propulsion resulting from a rich variety of shapes, forms, and swimming strategies. Here, we explore the variability of swimming speed for unicellular eukaryotes based on published data. The data naturally partitions into that from flagellates (with a small number of flagella) and from ciliates (with tens or more). Despite the morphological and size diff…
Suitable asymmetric microstructures can be used to control the direction of motion in microorganism populations. This rectification process makes it possible to accumulate swimmers in a region of space or to sort different swimmers. Here we study numerically how the separation process depends on the specific motility strategies of the microorganisms involved. Crucial properties such as the separation efficiency and the separation time for two bacterial strains are precisely defined and evaluated. In particular, the sorting of two bacterial populations inoculated in a box consisting of a series…
The motility of a cell can be triggered or inhibited not only by an applied force but also by a mechanically neutral force couple. This type of loading, represented by an applied stress and commonly interpreted as either squeezing or stretching, can originate from extrinsic interaction of a cell with its neighbors. To quantify the effect of applied stresses on cell motility we use an analytically transparent one-dimensional model accounting for active myosin contraction and induced actin turnover. We show that stretching can polarize static cells and initiate cell motility while squeezing can …
The experimental characterisation of the swimming statistics of populations of microorganisms or artificially propelled particles is essential for understanding the physics of active systems and their exploitation. Here, we construct a theoretical framework to extract information on the three-dimensional motion of micro-swimmers from the Intermediate Scattering Function (ISF) obtained from Differential Dynamic Microscopy (DDM). We derive theoretical expressions for the ISF of helical and oscillatory breaststroke swimmers, and test the theoretical framework by applying it to video sequences gen…
Phototaxis is an important reaction to light displayed by a wide range of motile microorganisms. Flagellated eukaryotic microalgae in particular, like the model organism Chlamydomonas reinhardtii, steer either towards or away from light by a rapid and precisely timed modulation of their flagellar activity. Cell steering, however, is only the beginning of a much longer process which ultimately allows cells to determine their light exposure history. This process is not well understood. Here we present a first quantitative study of the long timescale phototactic motility of Chlamydomonas at both …
Many microorganisms live and evolve in complex fluids. Examples include mammalian spermatozoa in cervical mucus, worms (e.g., \textit{C. elegans}) in wet soil, and bacteria (e.g., \textit{H. pylori}) in our stomach lining. Due to the presence of (bio)polymers and/or solids, such fluids often display nonlinear response to (shear) stresses including viscoelasticity and shear-rate dependent viscosity. The successful interaction between these microorganisms and their fluid environment is critical to the function of many biological processes including human reproduction, ecosystem dynamics, and the…
Many motile microorganisms react to environmental light cues with a variety of motility responses guiding cells towards better conditions for survival and growth. The use of spatial light modulators could help to elucidate the mechanisms of photo-movements while, at the same time, providing an efficient strategy to achieve spatial and temporal control of cell concentration. Here we demonstrate that millions of bacteria, genetically modified to swim smoothly with a light controllable speed, can be arranged into complex and reconfigurable density patterns using a digital light projector. We show…
Flagella and cilia are cellular appendages that inherit essential functions of microbial life including sensing and navigating the environment. In order to propel a swimming microorganism they displace the surrounding fluid by means of periodic motions, while precisely-timed modulations of their beating patterns enable the cell to steer towards or away from specific locations. Characterizing the dynamic forces, however, is challenging and typically relies on indirect experimental approaches. Here, we present direct in vivo measurements of the dynamic forces of motile Chlamydomonas reinhardtii …
The motility of microorganisms is influenced greatly by their hydrodynamic interactions with the fluidic environment they inhabit. We show by direct experimental observation of the bi-flagellated alga Chlamydomonas reinhardtii that fluid elasticity and viscosity strongly influence the beating pattern - the gait - and thereby control the propulsion speed. The beating frequency and the wave speed characterizing the cyclical bending are both enhanced by fluid elasticity. Despite these enhancements, the net swimming speed of the alga is hindered for fluids that are sufficiently elastic. The origin…
Seeing new depths: Three-dimensional flow of a free-swimming alga
University of Minnesota（明尼苏达大学）；National Institute for Mathematical Sciences（韩国数学科学研究所）；Chung-Ang University（中央大学）；University at Buffalo（布法罗纽约州立大学）；University of Cincinnati（辛辛那提大学）
Interactions between swimming cells and surfaces are essential to many microbiological processes, from bacterial biofilm formation to human fertilization. However, in spite of their fundamental importance, relatively little is known about the physical mechanisms that govern the scattering of flagellated or ciliated cells from solid surfaces. A more detailed understanding of these interactions promises not only new biological insights into structure and dynamics of flagella and cilia, but may also lead to new microfluidic techniques for controlling cell motility and microbial locomotion, with p…
Run-and-tumble motility is widely used by swimming microorganisms including numerous prokaryotic eukaryotic organisms. Here, we experimentally investigate the run-and-tumble dynamics of the bacterium E. coli in polymeric solutions. We find that even small amounts of polymer in solution can drastically change E. coli dynamics: cells tumble less and their velocity increases, leading to an enhancement in cell translational diffusion and a sudden decline in rotational diffusion. We show that suppression of tumbling is due to fluid viscosity while the enhancement in swimming speed is mainly due to …
Bacterial processes ranging from gene expression to motility and biofilm formation are constantly challenged by internal and external noise. While the importance of stochastic fluctuations has been appreciated for chemotaxis, it is currently believed that deterministic long-range fluid dynamical effects govern cell-cell and cell-surface scattering - the elementary events that lead to swarming and collective swimming in active suspensions and to the formation of biofilms. Here, we report the first direct measurements of the bacterial flow field generated by individual swimming Escherichia coli …
