Download Abstracts Worshop "Microorganisms in turbulent flows"

Participant name
Title and abstract
Bearon, Rachel
The transport of active swimmers in shear flows. Many micro-organisms
such as bacteria and algae swim in fluid environments. This swimming
behaviour can interact with fluid motions to generate transport which differs both
from that experienced by passive tracers in flow and micro-swimmers in the
absence of flow. Examples will include a mechanistic model for helical
gravitactic phytoplankton and a model for slender bacteria which undergo runand-tumble chemotaxis in a channel.
Bees, Martin
Orientation and dispersion of swimming microorganisms in laminar and
turbulent flows. To understand large-scale behavioural dynamics of plankton in
complex flows it is necessary to disentangle mechanisms for individual
behaviour, and systematically scale-up to a continuum or population-level
description of a suspension. Here, I shall describe how the coupling of external
torques and stimuli with micro- and macro-scale fluid dynamics can result in
effective biased motion, not necessarily in the intended direction, leading to
dispersion phenomena in laminar and turbulent flows that are qualitatively
distinct from tracer particles. New results will be presented for a population-level
description of the relative drift and diffusion of non-biased swimming cells in
flows in constrained environments.
Benzi, Roberto
Competition between fast and slow diffusing species. We study an
individual based model in which two spatially-distributed species, characterized
by different diffusivities, compete for resources. We consider several examples
with homogeneous and distributed resource and subject to compressible and
incompressible advection. In all cases, at varying the parameters, we observe a
transition from a regime in which diffusing faster confers an effective selective
advantage to one in which it constitutes a disadvantage. We analytically
estimate the magnitude of this advantage (or disadvantage) and test it by
measuring fixation probabilities in simulations of the individual-based model. Our
results provide a framework to quantify evolutionary pressure for increased or
decreased dispersal in a given environment.
Brandt, Luca
Numerical simulations of microorganisms in homogeneous turbulence:
chemical response and sedimentation.
Calzavarini, Enrico
A Lagrangian model of Copepod dynamics: clustering by escape jumps in
turbulence. Planktonic copepods are small crustaceans that have the ability to
swim by quick powerful jumps. Such an aptness is used to escape from high
shear regions, which may be caused either by flow perturbations, produced by a
large predator (i.e. fish larave), or by the inherent highly turbulent dynamics of
the ocean. Through a combined experimental and numerical study, we
investigate the impact of jumping behaviour on the small-scale patchiness of
copepods in a turbulent environment.
Crimaldi, John
Dynamics of Motile Phytoplankton in Turbulence: Experimental and
Numerical Investigations of Microscale Patchiness. The collective impact of
phytoplankton in biogeochemical cycles stems from interactions at the
microscale, and the nature of these interactions depends on the spatial
distribution of individual phytoplankton cells. Numerical simulations from the
Stocker lab (e.g., Durham et al., 2011) demonstrate that turbulence biases the
swimming direction of motile phytoplankton, resulting in the generation of
microscale patchiness. This unmixing process is driven by gyrotactic coupling
between Kolmogorov-scale velocity gradients and the phytoplankton motility; the
degree of generated patchiness depends both on features of the flow and the
organism. In this talk, I will discuss results and challenges from preliminary
experiments to directly visualize and measure microscale phytoplankton
distributions in realistic turbulent flows. Live populations of motile phytoplankton
were introduced into a purpose-built grid-turbulence facility that generates
approximately homogeneous, isotropic turbulence. Planar laser-induced
fluorescence (PLIF) was then used to image 2D distributions of individual cells,
enabling direct calculations of patchiness for two species and several flow
cases. Future work will extend these measurements to 3D for a wider range of
species and flows. I will also discuss numerical simulations of gyrotactic
aggregation to demonstrate the role of Lagrangian Coherent Structures (LCS)
on patch formation.
De Lillo, Filippo
Neutrally Buoyant Organisms in Stratified Turbulence. Numerical
simulations of a density-stratified, turbulent flow are employed to investigate the
formation of thin layers of non-swimming organisms around an equilibrium
depth, where their density equals that of the fluid. We find that the resulting
distribution has non-trivial properties beyond the simple vertical localization. The
consequences for the formation of thin phytoplankton layers are discussed.
De Monte, Silvia
On the distribution of rare marine microbial genetic sequences. Rare
species are an notable feature of communities, and their assessment influences
both the understanding of the ecological dynamics, and conservation policies.
Quantification of biodiversity strongly depends on the capacity of resolving rare
organisms, and hypothesis about the distribution of their abundance is often
used as a means of estimating biodiversity in cases of under-sampling.
Mathematical models on community composition generically predict that the
abundance of rare species decreases exponentially with their rank. This
behaviour is supported by observations of animal populations, in spite of the
relatively small number of different coexisting species. Molecular methods,
providing many hundreds of different genetic sequences per sample, open the
door to a more precise analysis of the tail of species of low abundance. Even if
the ‘rare biosphere’ is often associated to the existence of a long tail of rare
sequences, few studies have addressed the shape of such a tail, and provided
different results depending on the class of organism and environment under
study. In this talk, I will present evidence that the tail of rare sequences in marine
planktonic communities appear to follow a power law with a highly consistent
exponent in more than 50 locations of the global ocean, sampled during the Tara
oceans expedition. I will discuss different hypothesis on the mechanisms that
may shape planktonic communities across ecological and evolutionary time
scales.
Durham, M. William
Turbulent unmixing: how flow drives patchiness in the distribution of
phytoplankton. Phytoplankton are often heterogeneously distributed at the
centimeter scale, corresponding to the size of the smallest turbulent fluctuations.
We demonstrate that this patchiness can originate from a coupling between
turbulent shear and gyrotactic motility, a defining feature of many phytoplankton
species. By tracking individual cells within a direct numerical simulation (DNS) of
turbulence, we observed gyrotactic phytoplankton aggregate in tightly packed
clusters. The fate of a species is characterized by two dimensionless
parameters, measuring cell stability and swimming speed. These models are
confirmed with by measuring the distribution of Heterosigma akashiwo within a
vortical flow. By reducing the mean distance between organisms, this previously
unconsidered mechanism can markedly increase encounter rates, which control
nearly all ecological interactions in the ocean.
Karp-Boss, Lee
Phytoplankton sinking in turbulent flows. Turbulence is a ubiquitous and
important feature of the upper mixed layer where phytoplankton reside. On
scales relevant to individual cells and colonies, dissipating turbulence thins
diffusive boundary layers around cells and affects probabilities of encounter
critical for processes such as predator-prey interactions and aggregation. Superimposed on ambient fluid motion are local motions of cells due to
swimming and gravitational settling. Phytoplankton cells, particularly the large
and morphologically diverse, non-motile diatoms, are denser than their
surrounding fluid and therefore sink. Sinking holds significant implications to the
residence time of cells in the photic zone and ultimately to phytoplankton
productivity and fluxes of carbon and other elements to the deeper ocean. How
settling cells interact with ambient turbulence is not well understood. Results
from experimental and numerical studies show that turbulence enhances sinking
(or rising) velocities of a variety of particles including phytoplankton. In addition,
interactions between settling particles and turbulence can lead to clustering. Proposed explanations to the observed behaviors have focus on inertial
mechanisms of acceleration. However, in the parameter space defined by the
characteristics of phytoplankton, shape and buoyancy control may be much
more important than inertia in determining phytoplankton-turbulence
interactions. Kiørboe, Thomas
Small-scale turbulence and organism-organism interaction in the ocean.
Small-scale turbulence may enhance collision rates between microscopic
particles and organisms in the plankton and, thus, have direct implications for
fundamental ecological processes in the ocean, including formation of marine
snow and predator-prey encounter rates. Because many plankton perceive their
environment, including their prey and predators, through fluid signals, turbulence
may also interfere indirectly with organism interactions. I will review and discuss
experimental and theoretical evidence of such effects of small-scale turbulence.
Lauga, Eric
Fluid dynamics at the level of one cell
Many small organisms possess flagella, slender whiplike appendages which are
actuated in a periodic fashion in fluids and allow the cells to self-propel. In this
talk we highlight some interesting fluid dynamics phenomena at the level of one
cell and its flagella. We review the classical physics for flagellar propulsion,
summarise some classical examples where flow physics has successfully shed
light on biology, and focus on our recent work on the interactions between
multiple deforming flagella.
Mahadevan, Amala
Plankton Patchiness. The availability of light and nutrients essential to the
growth of phytoplankton are variable and modulated by the complex dynamics of
the upper ocean. Dynamical instabilities and changing surface conditions lead to
an evolving oceanic environment and turbulent flow field that support episodic
growth, while stirring and transporting phytoplankton. This results in a patchy
distribution of phytoplankton with a large fraction of the biological activity
concentrated in hotspots. Here, I will examine the variability of phytoplankton
concentrations on scales of 1-100 km using satellite and in situ data. Using
models for mixed layer dynamics and productivity, I will demonstrate physical
processes that modulate the conditions for phytoplankton growth on time scales
of order a day and solicit a strong biological response. I will argue that episodic
phytoplankton productivity and patchy distributions are triggered by ocean
dynamics and are critical to the ecosystem built on the success of organisms
that rely on the aggregation of food.
Mariani, Patrizio
Swimming under the risk of predation: plankton encounter rates and selfoverlap in calm and turbulent conditions. Movement is a fundamental
behavior of organisms that brings about beneficial encounters with resources
but also exposes them to dangers of predation. Those constraints and the
tradeoff between benefits and risks should shape the movement patterns
adopted by organisms. This tradeoff can be hypothesized as being particularly
apparent in the behavior of plankton, which inhabits a dilute 3D environment
where there are few refuges or orienting landmarks. In this talk I will present an
analysis of the swimming path geometries of plankton based on laboratory
observations and numerical modeling. A volumetric Monte Carlo sampling
approach is used to analyze 3D zooplankton tracks collected in calm water
conditions and to derive a self-overlap function. The self-overlap function
appears to reveal the tradeoffs between the efficient search for prey and
minimization of predation risk. The results demonstrate that swimming patterns
in plankton are highly correlated and display non-random properties that reduce
predation risk in pelagic environments and are consistent with lifetime fitness
optimization. Moreover, these behaviors differ between species and gender, and
change with local environmental conditions, indicating state and stage
dependent tradeoffs in movement behavior and suggesting efficient adaptive
behavior in planktonic organisms. We expand the approach introducing
turbulence in our analyses and describing the encounter dynamics of different
behavioral patterns in both calm and turbulent conditions. This is done using a
numerical agent-based model of the plankton encounter rate that is coupled to
kinematic simulations of the turbulent flow.
Nelson, David
Competition and cooperation at high Reynolds number. Microorganisms
living in the ocean can be subject to strong turbulence, with cell division times in
the middle of a Kolmogorov-like cascade of eddy turnover times. We start with
the dynamics of a diffusive Fisher equation describing cell proliferation in one
and two dimensions, coupled to turbulent advection. Inertial effects and cell
buoyancy lead us to study effectively compressible advecting velocity fields. For
strong enough compressible turbulence, reproducing microorganisms such as
bacteria and phytoplankton track, in a quasilocalized fashion, sinks in the
turbulent field, with important consequences for the carrying capacity and for
fixation times when two genetically different species compete. We describe a
model, inspired by experiments on baker's yeast, which focuses on both
competition and cooperation.
Pagonabarraga,
Ignacio
Hydrodynamic cooperativity in active suspensions: self organization and
cluster phase formation. Active systems generate motion due to energy
consumption, usually associated to their internal metabolism or to appropriate,
localized, interfacial chemical reactivity. As a result, these systems are
intrinsically out of equilibrium and their collective properties result as a balance
between their direct interactions and the indirect coupling to the medium in
which they displace. In many circumstances self-propelled particle swim and
move inside a fluid environment. The role of the medium in the collective
behavior of such systems remains less well understood. In particular, the effect it
may have modulating or modifying the understood mechanisms for selfassembly in their absence has not been properly addressed. A dynamical
approach is required to analyze the evolution of such active suspensions and
quantify their selfassembly and ability to generate intermediate and large scale
stable structures. The use of computational models that couple individuallyresolved self-propelling particles and the continuum solvent in which they move
provides a useful means to analyze and quantify the properties of spontaneous
emerging structures. I will describe how to take advantage of coarse grained
computational methods that capture the essence of activity generation and the
appropriate hydrodynamic coupling when ensembles of active particles move
together. I will analyze the relevant physical mechanisms underlying the
specific properties of model active suspensions. By focusing on simplified
models, it is possible to identify the relevant parameters which control such
behavior. Understanding the mechanical principles which determine the
emergence of cooperativity will provide a solid basis to clarify the role of
hydrodynamics in active materials and understand how to combine them with
biochemical interactions to control their properties and behavior.
Rafai, Salima
Flowing properties of a microswimmer suspension. Suspensions of motile
living organisms represent a non equilibrium system of condensed matter of
great interest on a fundamental point of view as well as for industrial
applications. These are suspensions composed of self-driven units - active
particles- able to convert stored energy into movement. Interactions between
active particles and the liquid they are swimming in give rise to mechanical
stresses and large scale collective motion that have recently attracted a lot of
interest in physics and mechanics communities. From the industrial point of
view, microalgae are used in many applications ranging from the food industry to
the development of new generations of biofuels. The biggest challenges
concerning all this applications are the separation, filtration and concentration
processes of microalgae. There is thus a real need of a better understanding of
the flow of active matter to achieve a optimal control of these systems. I’ll
present our recent work on microswimmer suspensions: rheological properties
of active suspensions as well as the « microscopic » characteristics of the
random walk of the green microalga Chlamydomonas Reinhardtii. We have
recently shown that hydrodynamics of a microalgae suspension coupled with
phototaxis* leads to a spontaneous concentration of the suspension toward the
center of the channel. Experiments as well as simulations will be presented.
*Biased movement that occurs when an organism moves in response to the
stimulus of light.
Schmitt, François
Plankton in marine turbulence. Marine planktonic organisms live in turbulent
flows and see the world in a Lagrangian way. They have developed, over many
generations, a strong adaptation to the fluctuations of the fluid they live in. The
results are complex behaviors and population dynamics. Here we propose an
overview of our previous results in two topics related to plankton complex
dynamics. First, we discuss phytoplankton concentration in relation with
turbulence, from field measurements. Florescence is a proxy of phytoplankton
concentration and can be recorded in situ, at high frequency (typically 1 Hz).
Fixed point as well as Lagrangian measurements of fluorescence have been
analyzed, and compared to temperature simultaneous measurements, which
belong to turbulent passive scalars. Scaling laws for the characterization of
intermittency are obtained, and depending on the scale, phytoplankton is seen
as been close to a passive scalar, or to behave as a chemically or biologically
active scalar. Such methodology is illustrated with several case studies,
recorded in Eulerian or Lagrangian way in the eastern English Channel. We also
discuss zooplankton behavior by considering copepods swimming statistics.
Copepods have developed, over a very large number of generations, swimming
abilities as trade-off between the energetic cost of swimming and the benefits of
swimming behavior, for mating, for food intake and for avoiding predators. The
swimming strategy is genetically programmed to adapt to the turbulent flow
corresponding to their ecological niche. In the experiments considered here,
copepods are taken from the field, placed in the laboratory in an aquarium, and
filmed. Image analysis provides access to trajectories, velocities, and in some
cases (when high speed cameras are used) acceleration. Copepod swimming
behavior is statistically characterized in the framework of anomalous diffusion
and multifractal random walks. Clustering is also performed to study the
behavior using symbolic dynamics. With such tools, copepod’s sex,
development stage, species, and environmental conditions may be considered.
Finally we also discuss the role of very large acceleration events as a predator
avoidance strategy, and analyse high speed (1000 frames per second) records
of jump events of the species Eurytemora affinis and Acartia tonsa: the statistics
of the jump duration, time between jumps, velocity and acceleration dynamics
during jump events, are considered for both species.
Stocker, Roman
How much fluid mechanics do phytoplankton know? There are now
multiple examples of the striking and important consequences of turbulence on
phytoplankton, including the formation of patchiness and the enhancement or
reduction of vertical migration rates. These arise due to diverse phenotypes,
including motility, cell elongation and asymmetric mass distribution. One may
argue that these effects result from phytoplankton "knowing" turbulence in an
evolutionary sense, where certain phenotypes have evolved to be attuned to
prevailing turbulence conditions. However, much less is known on whether
phytoplankton can actively respond to turbulence through changes in their
behavior. In other words, how much do phytoplankton know about turbulence in
an ecological sense? I present results that illustrate a striking, active response of
a phytoplankton population to turbulence-like cues in a carefully controlled
millifluidic 'flip chamber', showing that up to half of the cells alter their direction of
migration within minutes, possibly as a bet hedging strategy to escape
damaging turbulence microzones in the ocean. I suggest that this finding
renders efforts to understand the interaction of microorganisms and turbulence
both more complex and more intriguing.
Yamazaki, Hidekatsu Oceanic turbulence and phytoplankton dynamics. Phytoplankton requires
both light and nutrient, thus requires to stay in the upper ocean where
turbulence stirs water column. Turbulence mixes oceanic properties, such as
salinity and temperature. How does it mix phytoplankton? How do they
distribute in space? How small scale do we need to resolve the microscale
distribution? I have developed two types of fluorescence probe, LED (2 cm
resolution) and laser (2 mm resolution). I have found that the LED data are
significantly different from the laser data that exhibit highly intermittent features.
The local signals are considerably stronger than the spatially average signal. I
also mounted an optic system on the microstructure profiler TurboMAP-L to
identify the source of intermittent fluorescence signals and found the strong
signals came from marine aggregates. From ten different field campaigns I
compiled the average size of aggregate and the average rate of kinetic energy
dissipation rate and found they are positively correlated. The implications of the
field data are presented in my talk. Also I will introduce new plankton ecosystem
models that take microscale spatial heterogeneity into account.