ABOUT
The Microscale Ocean Biophysics crowd started a seminar series back in January 2021 as a way to keep the community in contact during the long hiatus caused by COVID. Talks are currently held once a month, either on the third or the last Tuesday at 11AM EST/5PM CET (or equivalent summer time). Time and day might change occasionally to accommodate the needs of the speaker.
Zoom links are sent via email a few days before the talk.
How do I subscribe?
There is a mailing list for the community. All announcements will be made through that. To register, please see info in the MAILING LIST tab.
Please notice that this mailing list replaces the old one!
Who is organising it?
Current organisers are Fouad El Baidouri, Marika Takeuchi and Aditya Nayak.
Previous organisers include: Shilpa Khatri, Marco Polin, Roi Holzman, Roberto Pioli, Sophie Zweifel, Jonas Słomka and François Peaudecerf.
Can I see past seminars?
We are happy to share on YouTube some of the past talks in the MOB Seminar Series. Talks up to May 2022 can be found here. More recent ones can be found in the new MOB channel. Although we strive to make past talks available, unfortunately not all of them are.
The Microscale Ocean Biophysics crowd started a seminar series back in January 2021 as a way to keep the community in contact during the long hiatus caused by COVID. Talks are currently held once a month, either on the third or the last Tuesday at 11AM EST/5PM CET (or equivalent summer time). Time and day might change occasionally to accommodate the needs of the speaker.
Zoom links are sent via email a few days before the talk.
How do I subscribe?
There is a mailing list for the community. All announcements will be made through that. To register, please see info in the MAILING LIST tab.
Please notice that this mailing list replaces the old one!
Who is organising it?
Current organisers are Fouad El Baidouri, Marika Takeuchi and Aditya Nayak.
Previous organisers include: Shilpa Khatri, Marco Polin, Roi Holzman, Roberto Pioli, Sophie Zweifel, Jonas Słomka and François Peaudecerf.
Can I see past seminars?
We are happy to share on YouTube some of the past talks in the MOB Seminar Series. Talks up to May 2022 can be found here. More recent ones can be found in the new MOB channel. Although we strive to make past talks available, unfortunately not all of them are.
UPCOMING SEMINARS
PAST SEMINARS
October 29, 2024.
Martina Dal Bello, Yale University.
The distribution of fast and slow-growing bacteria changes predictably with seawater temperature and salinity
The ocean harbor rich microbial communities that underpin the functioning of marine ecosystems. Nevertheless, the spatial and temporal patterns of variation in the structure of these communities and the underlying drivers are still unclear. In this talk, I will show that, in datasets of marine microbiomes collected along axes of temperature variation, increasing temperatures universally favor slower-growing bacteria. Using the outcome of laboratory experiments with enriched marine bacterial cultures, I will highlight that increasing salinity has the opposite effect, promoting faster-growing taxa. These results are all consistent with theoretical predictions of how temperature- and salinity- dependent changes in growth rates differentially modulate the impact of mortality on species abundances. Overall, our findings offer a general framework to link changes in growth rates promoted by key environmental variables to the structure of bacterial communities.
September 24, 2024.
Manu Prakash, Stanford University.
Hidden Comet-tails of Marine Snow Impede Ocean-based Carbon Sequestration.
Phytoplankton in the upper layer of the ocean agglomerates and sinks under gravity, giving rise to a natural carbon transport mechanism termed biological pump. The perpetual shower of soft and fragile marine snow in the ocean is estimated to be annually sequestering 2-4.5 gigatons of carbon from the atmosphere into the abyss, regulating both the atmospheric CO2 and the sustenance of marine ecosystems. A predictive underpinning of marine snow is thus crucial. But we currently lack a quantitative microphysics-based framework for the formation, sedimentation and remineralization of marine snow, leading to significant uncertainties in the current carbon flux estimates in climate models. By directly measuring the sinking velocities and detailed flows around individual marine snow particles, we discover a new morphological feature in marine snow – a physical invisible comet-tail forming a halo around a visible particulate matter during sedimentation. These hitherto unseen comet-tails are made of viscoelastic transparent exopolymer, that fundamentally modifies the sinking behavior. Our observations guide a new theoretical framework, based on Stokesian sedimentation, in which we include this previously invisible degree of freedom and construct a reduced order model for these compound particles. Furthermore, the combination of field experiments and theory enabled a sedimentation-based measurement of the elastic response of the mucus. We corroborate these findings with 3D volumetric imaging of marine snow particles, that illuminates the heterogeneous microstructure of marine snow. The discovery of multi-phase nature of marine snow and a new conceptual framework that incorporates the invisible degrees of freedom in the sedimentation dynamics lays the foundation for understanding the formation, sedimentation and remineralization of marine snow in the purview of physics. The crucial role of viscoelasticity of marine mucus as one of the knobs of carbon flux, opens rich possibilities for studying biological origin of mucus, and its complex rheology in the open oceans and potential bio-geoengineering remediation.
July 30, 2024.
Joseph Christie-Oleza, University of the Balearic Islands (Spain).
Pili in the oceans; new functions, new forms of movement.
How oligotrophic marine cyanobacteria position themselves in the water column is currently unknown. The current paradigm is that these organisms avoid sinking due to their reduced size and passive drift within currents. Here, we show that one in four picocyanobacteria encode a type IV pilus which allows these organisms to increase drag and remain suspended at optimal positions in the water column, as well as evade predation by grazers. The evolution of this sophisticated floatation mechanism in these purely planktonic streamlined microorganisms has important implications for our current understanding of microbial distribution in the oceans and predator–prey interactions which ultimately will need incorporating into future models of marine carbon flux dynamics.
June 25, 2024.
Elena Bollati, U. Copenhagen (Denmark).
The colours of the reef: microscale light management by coral pigments
Coral reefs are hotspots of biodiversity and productivity in tropical oceans. The foundation of these ecosystems is the symbiosis between corals and the dinoflagellate algae harboured intracellularly within their tissue. Photosynthesis by the algal symbionts is the primary source of nutrition for the coral host, hence corals have evolved a number of strategies to fine-tune their internal light environment and to optimize symbiont photosynthesis. One of these mechanisms involves a group of pigments homologous to the Green Fluorescent Protein (GFP), which are produced by the coral host and are responsible for the striking bright colours typical of coral reefs. Although their structure and optical properties are well characterized, the precise function and mechanisms of action of these pigments in corals are still a matter of debate. Using minimally invasive optical techniques we have investigated the role of GFP-like pigments in corals living under radically different light regimes: shallow, light-stressed habitats and deeper, light-limited mesophotic reefs. In shallow water, these proteins protect the symbionts from excess sunlight and may facilitate recovery after bleaching events. On mesophotic reefs, they broaden the light spectrum experienced by the symbionts and may enhance photosynthesis in shaded tissue areas. These mechanisms are important evidence of how corals and their symbionts have adapted to strong environmental gradients, and give us insights on how they may adapt to a changing climate in the future.
Title: TBA
April 20, 2024.
Ghita Guessous, UCSD.
Life on particles: spatiotemporal dynamics, and Allee effects
Even though most bacterial growth in the wild occurs in physically structured environments, most quantitative studies of growth have focused on planktonic cells consuming dissolved substrates, largely due to experimental convenience. To successfully consume a solid substrate, cells need to deploy a suite of functionalities such as attachment to particles, secretion of hydrolytic enzymes to generate labile molecules, replication through consuming these nutrients and finally detachment accompanied by motility or chemotaxis to facilitate the encounter with new nutrient patches. In this talk, we will present an experimental system of growth on chitin particles that allows for the characterization of the above processes. We will emphasize various bacterial strategies of particle degradation, including one that allows to overcome the colonization/dispersal tradeoff that’s often associated with growth on particles. Spatiotemporal models will allow us to formalize the concept of the “chitosphere”. We will explore the parameter space in initial conditions that allows for exponential growth and examine the properties of this phase transition between growth and extinction. By bridging experimental and theoretical approaches, we provide novel insights related to chitin degradation in particular and the lifestyles associated with growth on solid surfaces more generally.
March 19, 2024
Jean-Baptiste Raina
University of Sydney
Uncovering complex chemically mediated microbial behaviours
The ability of marine bacteria to direct their movement in response to chemical gradients influences inter-species interactions, nutrient turnover, and ecosystem productivity. While natural chemical hotspots produce gradients comprised of hundreds to thousands of different chemical compounds, we do not know how this chemical diversity affects the chemotactic responses of bacteria. I will present results from two studies that reveal some unexpected responses when bacteria are exposed to complex chemical mixtures. Using in situ and laboratory-based assays, we show that marine bacteria are strongly attracted to the abundant algal polysaccharide laminarin, but chemotaxis towards this large molecule is enhanced by dimethylsulfoniopropionate (DMSP), another ubiquitous algal-derived metabolite. Our results indicate that DMSP acts as a methyl donor for marine bacteria, increasing their gradient detection capacity and facilitating their access to polysaccharide patches. Using a novel chemotaxis choice assay, we then directly expose a model marine bacterium to four potent chemoattractants simultaneously (i.e., one monosaccharide and three amino acids). Although the bacterium is strongly chemotactic to each of these molecules in isolation, when these four molecules are provided simultaneously, the cells exhibit a striking response by swimming towards only one of them. These results start shedding light on the synergistic effects (e.g., laminarin and DMSP) and sharp chemical preferences modulating the behaviours of bacteria.
February 20, 2024
Mazi Jalaal
U. of Amsterdam
Underwater Light Show of Dinoflagellates and Water Plants: On the Interaction of Photosynthetic Organisms with Light
Photosynthetic systems have to adapt to the ever-changing conditions of their environment, leading to the evolution of intriguing strategies across scales, from cells to the organism. Using experiments and mathematical models, we will discuss how a water plant re-arrange the internal structure of cells by the active motion of chloroplasts, to remain efficient during photosynthesis. We will show that the chloroplasts can behave like densely packed light-sensitive active particles, whose non-gaussian athermal fluctuations can lead to various self-organization scenarios, including active glassy dynamics under dim lights and highly packed active clusters under intense light. Next, we will explore the interaction of a single cell dinoflagellate to various light conditions and discuss the similarities and differences to plant cells.
November 21st 2023
Wim van Egmond
Microphotographer (https://www.wimvanegmond.com/)Wim van Egmond is an artist whose work lies deceptively close to scientific work. Wim is fascinated by the almost artificial way how science depicts nature. He started his career as a visual autonomous artist, studied painting, and specialised in photography using optical techniques such as microscopy. He portrays microbes and makes micro-landscapes. He combines the skills of 19th century naturalists with modern digital techniques, initially with the aim to make autonomous work but often with one foot in the scientific world. Wim regularly collaborates with scientists and in recent years he has developed techniques to create unique movies and images of fungi and other soil organisms. Marine life is one of his favourite subjects so he will also show a series of images and movies of plankton and other microscopic organisms from the sea.
October 24th 2023
Daniel J. Repeta
Woods Hole Oceanographic Institution
Microbial Iron Limitation in the Ocean’s Twilight Zone
One of the major paradigm shifts in ocean biogeochemistry achieved over the past two decades is the recognition that iron limits primary production across approximately one third of the ocean’s surface. Below the sunlit euphotic zone, respiration of sinking organic matter rapidly regenerates nutrients, and microbial metabolism in this upper mesopelagic “twilight zone” (200-500 m) is limited by the delivery of labile organic carbon. In contrast to the large number of studies describing nutrient limitation in surface waters, very few studies have explored the potential for nutrient limitation to microbial growth in the mesopelagic. As part of the US GEOTRACES program to measure trace metal distributions across the North Pacific Ocean we measured the distribution and uptake of siderophores, biomarkers for microbial iron limitation. We found that siderophore concentrations were high in chronically iron-limited surface waters, but equally high in the twilight zone underlying the North and South Pacific subtropical gyres, key ecosystems in the global carbon cycle. Our data indicates that the more rapid regeneration of nitrate and phosphate relative to iron on sinking organic matter leads to widespread iron deficiency in bacteria inhabiting the twilight zone. These results expand the region of ocean’s water column where nutrients limit microbial metabolism to include the interior waters of the Pacific subtropical gyres.
September 19th 2023
Andrew G. Palmer
Florida Institute of Technology
Quorum Sensing in Chlamydomonas - A model unicellular eukaryote
The phenomenon of quorum sensing (QS) allows microorganisms to coordinate behaviors by coupling phenotypic switching to cell density. Examples of QS are ubiquitous among prokaryotes but significantly less observed in eukaryotes. Recently, we have determined that QS regulates swimming speed in the model photosynthetic unicellular eukaryote, Chlamydomonas reinhardtii. This suggests QS may be more widely distributed among aquatic eukaryotes that previously thought. Here I will present on our current understanding of this phenomenon in the genus Chlamydomonas as well as its potential impacts on microbial ecology and biotechnology.
July 25th 2023
Tom Solomon
Bucknell University
How is a swimming microbe like a forest fire?
We present experiments on the effects of laminar flows on the motion of swimming microbes and on the motion of the excitable Belousov-Zhabotinsky chemical reaction. A universal theoretical framework of active mixing predicts invariant manifolds -- “burning invariant manifolds” (BIMs) for front propagation and “swimming invariant manifolds” (SwIMs) for self-propelled tracers -- that act as one-way barriers for both of these systems. In fact, the problem of front propagation is a special case of the more general, active mixing theory. We present results from several experiments: (a) BIMs blocking reaction fronts in a range of 2-D and 3-D vortex-dominated flows; (b) SwIMs blocking motion of swimming bacteria and eukaryotic microbes in a microfluidic hyperbolic flow in a cross channel; and (c) on-going experiments about the behavior of swimming microbes in vortex flows.
June 20th 2023
Ron Shnapp
Ben Gurion University of the Negev
Copepods counter dispersion through mating interactions
Many copepod species reproduce sexually and require mating encounters to reproduce. However, copepod concentrations in the ocean are not sufficiently high for random motion to support the encounter rates needed to sustain their population. The solution to this is the fact that copepods, like many other plankton, form patchy distributions that increase local copepod concentrations and encounter rates [1]. However, the process by which these patchy distributions form over different scales is not completely understood. Our research focuses on explaining the occurrence of mating clusters, which are patchy distributions that span approximately one meter or less [2]. Specifically, male copepods actively search for reproductive females in their immediate vicinity to increase their mating encounter rates. However, this searching behavior should lead to a diffusive flux of copepods that could disrupt the patchiness of their distributions. Our work proposes that the specific way in which copepods interact with potential mating partners is what prevents the breakdown of patchy distributions. We use a numerical model that we recently developed to study the formation of patchy distributions and explore the model's parameter space to determine what is necessary for patchiness to be sustained [3]. We also compare the model's results with two laboratory measurements of 3D copepod trajectories [3, 4], finding that the model accurately predicts the observed behavior. These results support the hypothesis that small-scale patchiness is driven by animal behavior and explain how zooplankton achieve high mating encounter rates in their complex environment.
[1] B. Pinel-Alloul and A. Ghadouani (2007). Spatial heterogeneity of planktonic microorganisms in aquatic systems, 203-310, Springer Netherlands, Dordrecht.
[2] C. S. Davis, S. M. Gallager and A. R. Solow (1992). Science 257, 230-232.
[3] R. Shnapp, F. -G., Michalec, and Holzner, M. (2022). arXiv preprint arXiv:2205.08927.
[4] F.-G. Michalec et al. (2017). Proc. Natl. Acad. Sci. U.S.A. 114.52, E11199-E11207 ; F.-G. Michalec et al. (2020). eLife 9, e62014.
May 30th 2023
Lars Behrendt
University of Uppsala
Unraveling the link between abiotic stress and organismal responses
Predicting the impact of environmental factors, such as temperature or oxygen levels, on organisms poses a formidable challenge. This is especially challenging when studying marine microorganisms, as they exhibit diverse phenotypes and metabolic backgrounds, resulting in varied responses to environmental changes. In this presentation, I will introduce tools that help us start describe the complex relationship between environmental factors and biological heterogeneity. Firstly, I will present microfabrication-based techniques that enable us to create custom-made abiotic environments. By combining these techniques with optical measurements of physiological significance, we can investigate the immediate impact of abiotic environments on the metabolism of different types of unicellular organisms. Secondly, I will introduce the use of chemical sensing particles to simultaneously measure oxygen levels and flow across intricate biological surfaces like corals. This approach has uncovered a previously unreported phenomenon: that the ciliary movement among distinct coral polyps facilitates the distribution of oxygen from areas of production to areas of consumption. By utilizing these methods in combination, I contend that we can start to unravel the intricate interactions between environments, biological heterogeneity, and transport. This, in turn, will potentially yield fresh insights in fields like environmental toxicology, adaptive evolution, and microbial ecology.
April 18th 2023
Fabio Nudelman
University of Edinburgh
Exploring biomineralisation, from mineral formation to structure-properties relationship.
In Nature, organisms from all 5 kingdoms are well known to produce a wide range of mineralized tissues combining inorganic and organic materials that are used for a large number of functions. Examples are shells and coral skeletons that give protection for the animals, magnetic particles in bacteria used for navigation and vertebrate bone that provide mechanical support and protection for the body. In all cases, the precipitation and crystallisation of the inorganic materials are controlled by specialized proteins and polysaccharides, resulting in mineralized tissues with extraordinary morphologies and remarkable mechanical properties. Our research is aimed at understanding how organisms control the formation of such mineralized tissues, and how their properties arise from their structures. In the first part of the talk I will discuss our work on coccolithophore biomineralization. These organisms are unicellular marine algae that produce complex, disk-shaped structures made of CaCO3 called coccoliths. We used cryo-transmission electron microscopy and cryogenic ptychographic X-ray computed tomography, to study the mechanisms controlling crystal nucleation and morphology. In the second part of the talk, will discuss our research on brachiopod shells that are made of fluorapatite. These shells are hard and brittle when dry, and become soft and flexible when hydrated. Using ptychographic X-ray computed tomography, scanning electron microscopy and solid-state NMR, we characterized how the structure of the shells, from the micron to the molecular scales, changes upon the absorption of water leading to changes in mechanical properties.
March 28th 2023
Richard Henshaw
ETH Zurich
Swimming in a sea of viruses: elucidating the role of infected microbes on bacterial chemotaxis.
Viral infection of picophytoplankton is a principal driver of marine ecosystems and regulates nutrient cycling via the daily release of millions of tons of organic material from live biomass. Over 30% of marine cells are virusinfected (“virocells”), and whist viral-induced lysis is an established mechanism for transforming live biomass to more broadly available organic matter, prelysis infected microbes are frequently overlooked despite both their prevalence and a potential alternative nutrient in an otherwise sparse chemical landscape. To elucidate the role of virocells on marine microbial interactions, we combine long-term infection assays with metabolomic and microfluidic experiments to quantify both the chemical changes induced during pre-lysis infection and the subsequent impact on foraging of the surrounding microbial community. Firstly, a metabolomic analysis of exudates collected from infected cyanobacteria (Synechococcus) reveals time-dependent changes in the cell exudation during the infection cycle. Next, target compounds were identified and rapidly screened against a model marine chemotactic bacteria (Vibrio alginolyticus) using a novel parallelised chemotaxis microfluidic assay. Finally, bacterial chemotaxis to the infected/control cyanobacteria exudates is directly contrasted, demonstrating that the strongest chemotaxis response occurs extremely early in the infection cycle, prior to any cell-lysis. By combining the exudate chemotactic response with this newly established library of compound/concentration-specific chemotactic responses and integration of cross-disciplinary techniques, we have made significant strides towards understanding the viral impact on picophytoplankton organisms and its consequent ecological impacts.
February 21st 2023
Jules Jaffe
UC San Diego
From Physics to Physiology: Examples of how Imaging Can Inform Science
November 29th 2022
Francesca Malfatti
University of Trieste
Insights into the fitness of marine ballast-water Pseudomonas aeruginosa isolates: from small-scale interactions to secondary metabolite production.
Marine urbanized areas are harsh environments, home of many microbes. Harbor infrastructures, artificial polluted rivers (e.g., waste water, factories and power plant outflows) and ship surface thus including ballast water tank, structure the microscale world of "marine urbanized" microbes. In collaboration with OGS and ICGEB, we have started the exploration of fourteen 'sturdy' bugs, Pseudomonas aeruginosa, that have been isolated in harbour area and ballast water tanks in the N Adriatic Sea. At the microscale, every microbe to make a living needs to resist to antibiotics, escape from predators, explore the microenvironment, exploit nutrient sources, fight off other microbial competitors and produce antibiotics. I will present what we have discovered so far within the fitness framework for the marine Pseudomonas and two clinical isolates and discuss some data on genome architecture and future microscale experiments.
October 18th 2022
Jessie Levillain
PhD student at CMAP Ecole Polytechnique
Flagellar locomotion from a mathematical point of view
Swimming at the microscopic scale is a subject that has multiple links in several fields of science, ranging from biology to physics. The mathematics underlying to the many questions that arise have also opened up a field of research for a little less than fifteen years.
In particular many artificial swimmers have been proposed and studied in the literature [] showing swimming capabilities at low Reynolds numbers. As a sake of example, a simple mathematical model of microswimmers was introduced by Najafi and Golestanian [5], in which the swimmer consists in three spheres linked by rigid extensible arms, as shown in figure 1. This model was then extended to a three-sphere swimmer with a spring by Montino and DeSimone [4]. Following those ideas, we introduce a N-spring swimmer, consisting of an elongatable arm linked to a N mass-spring system. We study its limit model when N goes to infinity [2], and show a kind of elastic behavior for the tail. It turns out that the wave propagating along our one-dimensional swimmer is attenuated very quickly, contrarily to the behaviors observed in the tails of swimming microorganisms in biology.
A similar behavior was observed by Machin [3], which led to the conclusion that some form of activation along the flagella was needed [1]. We then focus on these flagellar activation mechanisms, from a mathematical point of view. In that direction, we recall the models, discussed in particular in [1] of molecular motors activating the bending of the flagellum. Then, we explain how to take into account the complex structure of the flagellum and in particular its influence on the tail’s oscillating pattern.
[1] F. Jülicher. Force and motion generation of molecular motors : A generic description. p. 46–74. doi :10.1007/bfb0104221.
[2] J. Levillain, F. Alouges, A. Lefebvre-Lepot. A limiting model for a low Reynolds number swimmer with N passive elastic arms. in preparation, 2022.
[3] K. E. Machin. Wave Propagation along Flagella. Journal of Experimental Biology, 35(4), 796–806, 1958. doi :10.1242/jeb.35.4.796.
[4] A. Montino, A. DeSimone. Three-sphere low-reynolds-number swimmer with a passive elastic arm. The European Physical Journal E, 38, 1–10, 2015.
[5] A. Najafi, R. Golestanian. Simple swimmer at low reynolds number : Three linked spheres. Phys. Rev. E, 69, 062901, 2004. doi :10.1103/PhysRevE.69.062901.
May 5th, 2022
Jeannette Yen
Georgia Institute of Technology (USA)
Small-scale biological-physical-chemical interactions in the plankton:
Wake signatures formed by prey, predators, mates, schoolmates at intermediate Re regimes
Fascinating studies of terrestrial locomotion by kangaroos, lizards and crabs, flight by bats, birds, and insects, and propulsion by fish, frogs, and flagellated organisms have stirred the imagination of biologists and provoked the curiosity of physical scientists. In response, we have engaged biological oceanographers and fluid dynamic engineers to perform similar studies of plankton. Plankton are aquatic organisms that form the base of the aquatic food web and therefore, aquatic ecosystem balance depends on their survival. The term plankton is derived from the Greek word πλανκτος ("planktos"), meaning "wanderer" or "drifter". From quantitative analyses of three-dimensional trajectories, propulsion and morphology, and small-scale turbulence, we learn that plankton often do not go with the flow. Plankton operate at intermediate Reynolds numbers, generating watery signals that can be attenuated by viscosity and confused with small-scale turbulence. Yet messages are created, transmitted, perceived and recognized. These messages guide essential survival tasks of aquatic organisms. At the small-scale where biologically-generated behavior differs from physically-derived flow, we find plankton self-propel themselves, are aware of each other, and evolve in response to the fluid environment in surprising ways.
Apr 7th, 2022.
Kevin Du Clos
U. Oregon (USA)
Unsteady sinking behavior in diatoms
Diatoms are a diverse and ubiquitous group of marine phytoplankton. They are encased in a silicate shell, making them more dense than seawater; their sinking is responsible for up to 40% of particulate organic carbon export in the ocean. Diatoms are not passive sinkers, however; they regulate their sinking speeds in response to their own biological states and to environmental factors, such as irradiance and nutrient concentrations. Video-based techniques enable the tracking of individual sinking cells, providing insights into how diatoms regulate sinking speeds over multiple time scales, including an unsteady sinking behavior in which diatoms oscillate sinking speeds within seconds. I will present results on the factors affecting the steady and unsteady sinking behavior of the centric diatom Coscinodiscus wailesii and some recent insights into sinking in other diatom taxa.
March 3rd, 2022.
Arezoo Ardekani
Purdue U. (USA)
Hydrodynamics-mediated trapping of microbes
The interaction of motile microorganisms and surrounding fluids is of importance in a variety of biological and environmental phenomena including the formation of marine algal blooms and bacterial bioremediation. Many microorganisms, especially bacteria, actively search for nutrients via a process called chemotaxis. The physical constraints posed by hydrodynamics in the locomotion of microorganisms can combine with their chemotactic ability to significantly affect functions like colonization of nutrient sources and their patchiness. Motivated by bacterial bioremediation of hydrocarbons released during oil spills, I will discuss the role of hydrodynamics toward dictating distribution of microbes around interfaces and drops in the presence and absence of surfactant. I will also discuss the role of density stratification on swimming and settling dynamics. Density stratification hampers the vertical flow and substantially affects the sedimentation, the hydrodynamic interactions between a pair, and the collective behavior of suspensions in various ways depending on the relative magnitude of stratification, inertia (advection), and viscous (diffusion) effects. We show that a swimmer can experience change of stability based on the relative importance of the above-mentioned effects.
Feb 2nd, 2022..
Oscar Guadayol
U. Lincoln (UK)
An engineering tool for a phytoplankton cell
Viscosity is critically important to planktonic life, as it affects both the rate of diffusion of molecules and the motility of microbes. And yet, it is a property that has been traditionally neglected by physical oceanography because water viscosity is well constrained by temperature, salinity and pressure. We know, however, that exopolymeric substances (EPS) released by marine organisms can alter the bulk viscosity of seawater at large scales. The role of EPS in physically structuring the microscale environment remains hypothetical. We used microrheological techniques to map viscosity with micron resolution around phytoplankton cells and inside aggregates, revealing the existence of steep gradients at the microscale. These gradients, as our numerical models show, can alter the dynamics and spatial structure of the chemical landscape and affect the motility and chemotactic performance of bacteria. Altogether this suggests that secreting EPS could be a good strategy for a phytoplankton cell to scaffold the phycosphere and optimize both resource acquisition and interactions with bacteria.
December 8th, 2021
Douglas Brumley
University of Melbourne
The role of bacterial chemotaxis in marine nutrient cycling and symbioses
Bacterial motility, symbioses, and marine nutrient cycling unfold at the scale of individual microorganisms, and are inherently dynamic. Moreover, microorganisms are routinely exposed to microscopic fluid flows, which have the capacity to influence motility and redistribute chemical cues. In this talk, I will outline how combining video-microscopy, image processing and mathematical modelling can resolve dynamic microscale processes which underpin the ecology of microorganisms. I will also demonstrate how the highly-resolved processes at the scale of individual cells can be connected to bulk measurements at the population-level.
October 7th, 2021
Julia Schwartzman
Parsons Laboratory
Department of Civil and Environmental Engineering
MIT
Cellular division of labor in self-organized collectives supports decomposition by a marine bacterium
The physical form life takes, from single cells to multicellular organisms, is central to its function. Self-organization, the process through which order emerges in biological systems from local interactions, underlies an astonishing array of complex biological functions ranging from resource partitioning to environmental resilience to reproduction. In this talk, I will discuss how self-organization scaffolds a cellular division of labor in clonal collectives of a polysaccharide-degrading marine bacterium. I will present experiments and simulations supporting the ideas that cell-density dependent cooperation and competition cue phenotypic specialization within clonal collectives, that interaction of cell types leads to the self-organization of clonal collectives into structurally complex forms, and that this emergent structure scaffolds a division of labor that supports cycles of growth and dispersal.
September 21st, 2021
Anders Andersen
Centre for Ocean Life
National Institute of Aquatic Resources
Technical University of Denmark
Feeding flow and membranelle filtration in ciliates
Ciliates are ubiquitous in the marine environment and important consumers of phytoplankton and flagellates. The feeding in ciliates is complex and relies in many species on coordinated motion in bands of transversal rows of cilia known as membranelles. We explore the feeding in the ciliate Euplotes vannus that uses a single membranelle band to both generate feeding flow, retain food particles, and transport them to the mouth region. To obtain a mechanistic understanding of the feeding, we use high-speed video-microscopy. The cilia move parallel to the membranelle band towards the mouth region in the power strokes, and a metachronal wave propagates away from the mouth region parallel to the band and outwards along the membranelles. From the inside of the band, a gap therefore opens between neighboring membranelles, and while food particles are retained, water is drawn in and pushed across the membranelle band as the gap closes from the inside. We rationalize our findings in a model that compares favorably with our observations of clearance rate and membranelle motion.
This is joint work with Mads Rode and Thomas Kiørboe.
May 13th, 2021
Knut Drescher
Biozentrum
Universität Basel
Triggers and mechanisms of biofilm dispersal of Vibrio cholerae
Bacteria can generate benefits for themselves and their kin by living in multicellular, matrix-enclosed communities, termed biofilms. The decision-making strategies used by bacteria to weigh the costs between remaining in a biofilm or actively dispersing are largely unclear, even though the dispersal transition is a central aspect of the biofilm life cycle. Using a highly controlled flow system for biofilm cultivation and environmental control, I will first demonstrate our understand of the signals that trigger Vibrio cholerae biofilm dispersal, before showing how exactly cells actively disperse from the biofilm matrix.
April 8th, 2021
Nawish Wadhwa
Harvard University
The bacterial flagellar engine has an automatic gearshift
Motility is critical for the survival and dispersal of bacteria, and it plays an important role during infection. Regulation of bacterial motility via chemotaxis and gene regulation is well studied. However, recent work has added a new dimension to this problem. The flagellar motor of bacteria autonomously assembles and disassembles torque-generating stator units in response to changes in the external viscous load. In Escherichia coli, up to 11 stator units drive the motor at high load while all the stator units are released at low load. We study this process by artificially manipulating the motor load using electrorotation, where a high frequency rotating electric field applies an external torque on the flagellar motor (1). Using this technique, we can increase or decrease the motor load at will and measure the resulting stator remodeling. We measured stator remodeling in both clockwise and counterclockwise rotating motors, and found that the motor’s response has a conserved torque dependence (2). We built a model that captures the observed dynamics and provides insight into the underlying molecular interactions. Torque-dependent stator remodeling takes place within tens of seconds, making it a highly responsive autonomous control mechanism.
1. Wadhwa, N., Phillips, R., & Berg, H. C. (2019). Torque-dependent remodeling of the bacterial flagellar motor. PNAS, 116(24), 11764-11769.
2. Wadhwa, N., Tu, Y., & Berg, H. C. (2021). Mechanosensitive remodeling of the bacterial flagellar motor is independent of direction of rotation. PNAS, 118(15) e2024608118.
March 22, 2021
Yuval Jacobi
The Division of Environmental, Water and Agricultural Engineering, Technion – Israel Institute of Technology
and
School of Marine Sciences, Ruppin Academic Center
Evasive microalgae: surface interaction in suspension feeding by ascidians
Ascidians are benthic suspension feeders that feed by filtering seawater using a mucous filter. In the past, the efficiency and rate of particle capture by ascidians was considered to be governed by particle size and the pore size of the mucous filter. By measuring the particle capture efficiency of several ascidian species, in-situ, we found that ultraplankton cells (bacteria and microalgae sized 0.2-10 µm) are captured at a significantly lower efficiency compared with similar sized polystyrene microspheres (0.3-10 µm). This phenomenon was observed both with particles and microbes that are smaller than the proposed pore size of the ascidian filter and, surprisingly, also for particles that are larger than the proposed pore size. In addition, we found that altering the surface properties of polystyrene microspheres by coating them with long-chain nonionic surfactants can lead to a reduction in capture efficiency, if the size of the surfactant’s hydrophilic chain is between 280 Da and 12 kDa.
Using particle-tracking confocal microscopy, we measured the Brownian motion of polystyrene particles embedded in fresh mucus harvested from the ascidian Herdmania momus. Results indicate that the mobility of equal-sized particles, possessing different surface properties, correlates well with their capture efficiency by H. momus. This finding serves as direct evidence of the role played by surface interactions in determining particle capture by ascidians. Images of the ascidian mucus, obtained via cryogenic scanning electron microscopy, combined with the fact that large microbes (larger than the estimated pore size) are not always captured at 100% efficiency, suggest that the structure of the ascidian mucous filter may be different from the rectangular mesh previously suggested. Our results show that surface interactions have an important role in mucus-based suspension feeding. Furthermore, given the lack of a known particle selection mechanism in ascidians, we propose that some microbial plankton possess surface traits that increase their mobility inside the mucous filter. This mobility enables the crossing of some cells to the down-stream side of the filter and out to sea, and thus serves as a strategy for evading predation.
February 11th, 2021
Mimi Koehl
Department of Integrative Biology
University of California, Berkeley
Locomoting in a turbulent environment: Ways to study microscale processes in a large-scale ocean
A major challenge in studying ocean biophysics is integrating the different scales at which various physical and biological processes occur. How can we make large-scale field measurements and models that include the behaviors and physical features of real organisms? Conversely, how can we design small-scale experiments to measure those biological factors under hydrodynamic conditions that reflect what the organisms actually experience in the large-scale ocean? I will discuss examples of some of the approaches we have used to span different scales in our studies of how microscopic animals locomote in turbulent ambient water flow. We have been using the microscopic larvae of bottom-dwelling marine animals to explore how the interaction between the swimming or crawling by an organism and the turbulent water flow around them determines how they move through the environment.
- Nov. 26, 2024. Flora Vincent, EMBL Heidelberg. Title: Single cell ecology to understand microbial interactions in the Ocean.
- Jan 28, 2025. Assaf Vardi, Weizmann Institute. Title: TBD.
PAST SEMINARS
October 29, 2024.
Martina Dal Bello, Yale University.
The distribution of fast and slow-growing bacteria changes predictably with seawater temperature and salinity
The ocean harbor rich microbial communities that underpin the functioning of marine ecosystems. Nevertheless, the spatial and temporal patterns of variation in the structure of these communities and the underlying drivers are still unclear. In this talk, I will show that, in datasets of marine microbiomes collected along axes of temperature variation, increasing temperatures universally favor slower-growing bacteria. Using the outcome of laboratory experiments with enriched marine bacterial cultures, I will highlight that increasing salinity has the opposite effect, promoting faster-growing taxa. These results are all consistent with theoretical predictions of how temperature- and salinity- dependent changes in growth rates differentially modulate the impact of mortality on species abundances. Overall, our findings offer a general framework to link changes in growth rates promoted by key environmental variables to the structure of bacterial communities.
September 24, 2024.
Manu Prakash, Stanford University.
Hidden Comet-tails of Marine Snow Impede Ocean-based Carbon Sequestration.
Phytoplankton in the upper layer of the ocean agglomerates and sinks under gravity, giving rise to a natural carbon transport mechanism termed biological pump. The perpetual shower of soft and fragile marine snow in the ocean is estimated to be annually sequestering 2-4.5 gigatons of carbon from the atmosphere into the abyss, regulating both the atmospheric CO2 and the sustenance of marine ecosystems. A predictive underpinning of marine snow is thus crucial. But we currently lack a quantitative microphysics-based framework for the formation, sedimentation and remineralization of marine snow, leading to significant uncertainties in the current carbon flux estimates in climate models. By directly measuring the sinking velocities and detailed flows around individual marine snow particles, we discover a new morphological feature in marine snow – a physical invisible comet-tail forming a halo around a visible particulate matter during sedimentation. These hitherto unseen comet-tails are made of viscoelastic transparent exopolymer, that fundamentally modifies the sinking behavior. Our observations guide a new theoretical framework, based on Stokesian sedimentation, in which we include this previously invisible degree of freedom and construct a reduced order model for these compound particles. Furthermore, the combination of field experiments and theory enabled a sedimentation-based measurement of the elastic response of the mucus. We corroborate these findings with 3D volumetric imaging of marine snow particles, that illuminates the heterogeneous microstructure of marine snow. The discovery of multi-phase nature of marine snow and a new conceptual framework that incorporates the invisible degrees of freedom in the sedimentation dynamics lays the foundation for understanding the formation, sedimentation and remineralization of marine snow in the purview of physics. The crucial role of viscoelasticity of marine mucus as one of the knobs of carbon flux, opens rich possibilities for studying biological origin of mucus, and its complex rheology in the open oceans and potential bio-geoengineering remediation.
July 30, 2024.
Joseph Christie-Oleza, University of the Balearic Islands (Spain).
Pili in the oceans; new functions, new forms of movement.
How oligotrophic marine cyanobacteria position themselves in the water column is currently unknown. The current paradigm is that these organisms avoid sinking due to their reduced size and passive drift within currents. Here, we show that one in four picocyanobacteria encode a type IV pilus which allows these organisms to increase drag and remain suspended at optimal positions in the water column, as well as evade predation by grazers. The evolution of this sophisticated floatation mechanism in these purely planktonic streamlined microorganisms has important implications for our current understanding of microbial distribution in the oceans and predator–prey interactions which ultimately will need incorporating into future models of marine carbon flux dynamics.
June 25, 2024.
Elena Bollati, U. Copenhagen (Denmark).
The colours of the reef: microscale light management by coral pigments
Coral reefs are hotspots of biodiversity and productivity in tropical oceans. The foundation of these ecosystems is the symbiosis between corals and the dinoflagellate algae harboured intracellularly within their tissue. Photosynthesis by the algal symbionts is the primary source of nutrition for the coral host, hence corals have evolved a number of strategies to fine-tune their internal light environment and to optimize symbiont photosynthesis. One of these mechanisms involves a group of pigments homologous to the Green Fluorescent Protein (GFP), which are produced by the coral host and are responsible for the striking bright colours typical of coral reefs. Although their structure and optical properties are well characterized, the precise function and mechanisms of action of these pigments in corals are still a matter of debate. Using minimally invasive optical techniques we have investigated the role of GFP-like pigments in corals living under radically different light regimes: shallow, light-stressed habitats and deeper, light-limited mesophotic reefs. In shallow water, these proteins protect the symbionts from excess sunlight and may facilitate recovery after bleaching events. On mesophotic reefs, they broaden the light spectrum experienced by the symbionts and may enhance photosynthesis in shaded tissue areas. These mechanisms are important evidence of how corals and their symbionts have adapted to strong environmental gradients, and give us insights on how they may adapt to a changing climate in the future.
Title: TBA
April 20, 2024.
Ghita Guessous, UCSD.
Life on particles: spatiotemporal dynamics, and Allee effects
Even though most bacterial growth in the wild occurs in physically structured environments, most quantitative studies of growth have focused on planktonic cells consuming dissolved substrates, largely due to experimental convenience. To successfully consume a solid substrate, cells need to deploy a suite of functionalities such as attachment to particles, secretion of hydrolytic enzymes to generate labile molecules, replication through consuming these nutrients and finally detachment accompanied by motility or chemotaxis to facilitate the encounter with new nutrient patches. In this talk, we will present an experimental system of growth on chitin particles that allows for the characterization of the above processes. We will emphasize various bacterial strategies of particle degradation, including one that allows to overcome the colonization/dispersal tradeoff that’s often associated with growth on particles. Spatiotemporal models will allow us to formalize the concept of the “chitosphere”. We will explore the parameter space in initial conditions that allows for exponential growth and examine the properties of this phase transition between growth and extinction. By bridging experimental and theoretical approaches, we provide novel insights related to chitin degradation in particular and the lifestyles associated with growth on solid surfaces more generally.
March 19, 2024
Jean-Baptiste Raina
University of Sydney
Uncovering complex chemically mediated microbial behaviours
The ability of marine bacteria to direct their movement in response to chemical gradients influences inter-species interactions, nutrient turnover, and ecosystem productivity. While natural chemical hotspots produce gradients comprised of hundreds to thousands of different chemical compounds, we do not know how this chemical diversity affects the chemotactic responses of bacteria. I will present results from two studies that reveal some unexpected responses when bacteria are exposed to complex chemical mixtures. Using in situ and laboratory-based assays, we show that marine bacteria are strongly attracted to the abundant algal polysaccharide laminarin, but chemotaxis towards this large molecule is enhanced by dimethylsulfoniopropionate (DMSP), another ubiquitous algal-derived metabolite. Our results indicate that DMSP acts as a methyl donor for marine bacteria, increasing their gradient detection capacity and facilitating their access to polysaccharide patches. Using a novel chemotaxis choice assay, we then directly expose a model marine bacterium to four potent chemoattractants simultaneously (i.e., one monosaccharide and three amino acids). Although the bacterium is strongly chemotactic to each of these molecules in isolation, when these four molecules are provided simultaneously, the cells exhibit a striking response by swimming towards only one of them. These results start shedding light on the synergistic effects (e.g., laminarin and DMSP) and sharp chemical preferences modulating the behaviours of bacteria.
February 20, 2024
Mazi Jalaal
U. of Amsterdam
Underwater Light Show of Dinoflagellates and Water Plants: On the Interaction of Photosynthetic Organisms with Light
Photosynthetic systems have to adapt to the ever-changing conditions of their environment, leading to the evolution of intriguing strategies across scales, from cells to the organism. Using experiments and mathematical models, we will discuss how a water plant re-arrange the internal structure of cells by the active motion of chloroplasts, to remain efficient during photosynthesis. We will show that the chloroplasts can behave like densely packed light-sensitive active particles, whose non-gaussian athermal fluctuations can lead to various self-organization scenarios, including active glassy dynamics under dim lights and highly packed active clusters under intense light. Next, we will explore the interaction of a single cell dinoflagellate to various light conditions and discuss the similarities and differences to plant cells.
November 21st 2023
Wim van Egmond
Microphotographer (https://www.wimvanegmond.com/)Wim van Egmond is an artist whose work lies deceptively close to scientific work. Wim is fascinated by the almost artificial way how science depicts nature. He started his career as a visual autonomous artist, studied painting, and specialised in photography using optical techniques such as microscopy. He portrays microbes and makes micro-landscapes. He combines the skills of 19th century naturalists with modern digital techniques, initially with the aim to make autonomous work but often with one foot in the scientific world. Wim regularly collaborates with scientists and in recent years he has developed techniques to create unique movies and images of fungi and other soil organisms. Marine life is one of his favourite subjects so he will also show a series of images and movies of plankton and other microscopic organisms from the sea.
October 24th 2023
Daniel J. Repeta
Woods Hole Oceanographic Institution
Microbial Iron Limitation in the Ocean’s Twilight Zone
One of the major paradigm shifts in ocean biogeochemistry achieved over the past two decades is the recognition that iron limits primary production across approximately one third of the ocean’s surface. Below the sunlit euphotic zone, respiration of sinking organic matter rapidly regenerates nutrients, and microbial metabolism in this upper mesopelagic “twilight zone” (200-500 m) is limited by the delivery of labile organic carbon. In contrast to the large number of studies describing nutrient limitation in surface waters, very few studies have explored the potential for nutrient limitation to microbial growth in the mesopelagic. As part of the US GEOTRACES program to measure trace metal distributions across the North Pacific Ocean we measured the distribution and uptake of siderophores, biomarkers for microbial iron limitation. We found that siderophore concentrations were high in chronically iron-limited surface waters, but equally high in the twilight zone underlying the North and South Pacific subtropical gyres, key ecosystems in the global carbon cycle. Our data indicates that the more rapid regeneration of nitrate and phosphate relative to iron on sinking organic matter leads to widespread iron deficiency in bacteria inhabiting the twilight zone. These results expand the region of ocean’s water column where nutrients limit microbial metabolism to include the interior waters of the Pacific subtropical gyres.
September 19th 2023
Andrew G. Palmer
Florida Institute of Technology
Quorum Sensing in Chlamydomonas - A model unicellular eukaryote
The phenomenon of quorum sensing (QS) allows microorganisms to coordinate behaviors by coupling phenotypic switching to cell density. Examples of QS are ubiquitous among prokaryotes but significantly less observed in eukaryotes. Recently, we have determined that QS regulates swimming speed in the model photosynthetic unicellular eukaryote, Chlamydomonas reinhardtii. This suggests QS may be more widely distributed among aquatic eukaryotes that previously thought. Here I will present on our current understanding of this phenomenon in the genus Chlamydomonas as well as its potential impacts on microbial ecology and biotechnology.
July 25th 2023
Tom Solomon
Bucknell University
How is a swimming microbe like a forest fire?
We present experiments on the effects of laminar flows on the motion of swimming microbes and on the motion of the excitable Belousov-Zhabotinsky chemical reaction. A universal theoretical framework of active mixing predicts invariant manifolds -- “burning invariant manifolds” (BIMs) for front propagation and “swimming invariant manifolds” (SwIMs) for self-propelled tracers -- that act as one-way barriers for both of these systems. In fact, the problem of front propagation is a special case of the more general, active mixing theory. We present results from several experiments: (a) BIMs blocking reaction fronts in a range of 2-D and 3-D vortex-dominated flows; (b) SwIMs blocking motion of swimming bacteria and eukaryotic microbes in a microfluidic hyperbolic flow in a cross channel; and (c) on-going experiments about the behavior of swimming microbes in vortex flows.
June 20th 2023
Ron Shnapp
Ben Gurion University of the Negev
Copepods counter dispersion through mating interactions
Many copepod species reproduce sexually and require mating encounters to reproduce. However, copepod concentrations in the ocean are not sufficiently high for random motion to support the encounter rates needed to sustain their population. The solution to this is the fact that copepods, like many other plankton, form patchy distributions that increase local copepod concentrations and encounter rates [1]. However, the process by which these patchy distributions form over different scales is not completely understood. Our research focuses on explaining the occurrence of mating clusters, which are patchy distributions that span approximately one meter or less [2]. Specifically, male copepods actively search for reproductive females in their immediate vicinity to increase their mating encounter rates. However, this searching behavior should lead to a diffusive flux of copepods that could disrupt the patchiness of their distributions. Our work proposes that the specific way in which copepods interact with potential mating partners is what prevents the breakdown of patchy distributions. We use a numerical model that we recently developed to study the formation of patchy distributions and explore the model's parameter space to determine what is necessary for patchiness to be sustained [3]. We also compare the model's results with two laboratory measurements of 3D copepod trajectories [3, 4], finding that the model accurately predicts the observed behavior. These results support the hypothesis that small-scale patchiness is driven by animal behavior and explain how zooplankton achieve high mating encounter rates in their complex environment.
[1] B. Pinel-Alloul and A. Ghadouani (2007). Spatial heterogeneity of planktonic microorganisms in aquatic systems, 203-310, Springer Netherlands, Dordrecht.
[2] C. S. Davis, S. M. Gallager and A. R. Solow (1992). Science 257, 230-232.
[3] R. Shnapp, F. -G., Michalec, and Holzner, M. (2022). arXiv preprint arXiv:2205.08927.
[4] F.-G. Michalec et al. (2017). Proc. Natl. Acad. Sci. U.S.A. 114.52, E11199-E11207 ; F.-G. Michalec et al. (2020). eLife 9, e62014.
May 30th 2023
Lars Behrendt
University of Uppsala
Unraveling the link between abiotic stress and organismal responses
Predicting the impact of environmental factors, such as temperature or oxygen levels, on organisms poses a formidable challenge. This is especially challenging when studying marine microorganisms, as they exhibit diverse phenotypes and metabolic backgrounds, resulting in varied responses to environmental changes. In this presentation, I will introduce tools that help us start describe the complex relationship between environmental factors and biological heterogeneity. Firstly, I will present microfabrication-based techniques that enable us to create custom-made abiotic environments. By combining these techniques with optical measurements of physiological significance, we can investigate the immediate impact of abiotic environments on the metabolism of different types of unicellular organisms. Secondly, I will introduce the use of chemical sensing particles to simultaneously measure oxygen levels and flow across intricate biological surfaces like corals. This approach has uncovered a previously unreported phenomenon: that the ciliary movement among distinct coral polyps facilitates the distribution of oxygen from areas of production to areas of consumption. By utilizing these methods in combination, I contend that we can start to unravel the intricate interactions between environments, biological heterogeneity, and transport. This, in turn, will potentially yield fresh insights in fields like environmental toxicology, adaptive evolution, and microbial ecology.
April 18th 2023
Fabio Nudelman
University of Edinburgh
Exploring biomineralisation, from mineral formation to structure-properties relationship.
In Nature, organisms from all 5 kingdoms are well known to produce a wide range of mineralized tissues combining inorganic and organic materials that are used for a large number of functions. Examples are shells and coral skeletons that give protection for the animals, magnetic particles in bacteria used for navigation and vertebrate bone that provide mechanical support and protection for the body. In all cases, the precipitation and crystallisation of the inorganic materials are controlled by specialized proteins and polysaccharides, resulting in mineralized tissues with extraordinary morphologies and remarkable mechanical properties. Our research is aimed at understanding how organisms control the formation of such mineralized tissues, and how their properties arise from their structures. In the first part of the talk I will discuss our work on coccolithophore biomineralization. These organisms are unicellular marine algae that produce complex, disk-shaped structures made of CaCO3 called coccoliths. We used cryo-transmission electron microscopy and cryogenic ptychographic X-ray computed tomography, to study the mechanisms controlling crystal nucleation and morphology. In the second part of the talk, will discuss our research on brachiopod shells that are made of fluorapatite. These shells are hard and brittle when dry, and become soft and flexible when hydrated. Using ptychographic X-ray computed tomography, scanning electron microscopy and solid-state NMR, we characterized how the structure of the shells, from the micron to the molecular scales, changes upon the absorption of water leading to changes in mechanical properties.
March 28th 2023
Richard Henshaw
ETH Zurich
Swimming in a sea of viruses: elucidating the role of infected microbes on bacterial chemotaxis.
Viral infection of picophytoplankton is a principal driver of marine ecosystems and regulates nutrient cycling via the daily release of millions of tons of organic material from live biomass. Over 30% of marine cells are virusinfected (“virocells”), and whist viral-induced lysis is an established mechanism for transforming live biomass to more broadly available organic matter, prelysis infected microbes are frequently overlooked despite both their prevalence and a potential alternative nutrient in an otherwise sparse chemical landscape. To elucidate the role of virocells on marine microbial interactions, we combine long-term infection assays with metabolomic and microfluidic experiments to quantify both the chemical changes induced during pre-lysis infection and the subsequent impact on foraging of the surrounding microbial community. Firstly, a metabolomic analysis of exudates collected from infected cyanobacteria (Synechococcus) reveals time-dependent changes in the cell exudation during the infection cycle. Next, target compounds were identified and rapidly screened against a model marine chemotactic bacteria (Vibrio alginolyticus) using a novel parallelised chemotaxis microfluidic assay. Finally, bacterial chemotaxis to the infected/control cyanobacteria exudates is directly contrasted, demonstrating that the strongest chemotaxis response occurs extremely early in the infection cycle, prior to any cell-lysis. By combining the exudate chemotactic response with this newly established library of compound/concentration-specific chemotactic responses and integration of cross-disciplinary techniques, we have made significant strides towards understanding the viral impact on picophytoplankton organisms and its consequent ecological impacts.
February 21st 2023
Jules Jaffe
UC San Diego
From Physics to Physiology: Examples of how Imaging Can Inform Science
November 29th 2022
Francesca Malfatti
University of Trieste
Insights into the fitness of marine ballast-water Pseudomonas aeruginosa isolates: from small-scale interactions to secondary metabolite production.
Marine urbanized areas are harsh environments, home of many microbes. Harbor infrastructures, artificial polluted rivers (e.g., waste water, factories and power plant outflows) and ship surface thus including ballast water tank, structure the microscale world of "marine urbanized" microbes. In collaboration with OGS and ICGEB, we have started the exploration of fourteen 'sturdy' bugs, Pseudomonas aeruginosa, that have been isolated in harbour area and ballast water tanks in the N Adriatic Sea. At the microscale, every microbe to make a living needs to resist to antibiotics, escape from predators, explore the microenvironment, exploit nutrient sources, fight off other microbial competitors and produce antibiotics. I will present what we have discovered so far within the fitness framework for the marine Pseudomonas and two clinical isolates and discuss some data on genome architecture and future microscale experiments.
October 18th 2022
Jessie Levillain
PhD student at CMAP Ecole Polytechnique
Flagellar locomotion from a mathematical point of view
Swimming at the microscopic scale is a subject that has multiple links in several fields of science, ranging from biology to physics. The mathematics underlying to the many questions that arise have also opened up a field of research for a little less than fifteen years.
In particular many artificial swimmers have been proposed and studied in the literature [] showing swimming capabilities at low Reynolds numbers. As a sake of example, a simple mathematical model of microswimmers was introduced by Najafi and Golestanian [5], in which the swimmer consists in three spheres linked by rigid extensible arms, as shown in figure 1. This model was then extended to a three-sphere swimmer with a spring by Montino and DeSimone [4]. Following those ideas, we introduce a N-spring swimmer, consisting of an elongatable arm linked to a N mass-spring system. We study its limit model when N goes to infinity [2], and show a kind of elastic behavior for the tail. It turns out that the wave propagating along our one-dimensional swimmer is attenuated very quickly, contrarily to the behaviors observed in the tails of swimming microorganisms in biology.
A similar behavior was observed by Machin [3], which led to the conclusion that some form of activation along the flagella was needed [1]. We then focus on these flagellar activation mechanisms, from a mathematical point of view. In that direction, we recall the models, discussed in particular in [1] of molecular motors activating the bending of the flagellum. Then, we explain how to take into account the complex structure of the flagellum and in particular its influence on the tail’s oscillating pattern.
[1] F. Jülicher. Force and motion generation of molecular motors : A generic description. p. 46–74. doi :10.1007/bfb0104221.
[2] J. Levillain, F. Alouges, A. Lefebvre-Lepot. A limiting model for a low Reynolds number swimmer with N passive elastic arms. in preparation, 2022.
[3] K. E. Machin. Wave Propagation along Flagella. Journal of Experimental Biology, 35(4), 796–806, 1958. doi :10.1242/jeb.35.4.796.
[4] A. Montino, A. DeSimone. Three-sphere low-reynolds-number swimmer with a passive elastic arm. The European Physical Journal E, 38, 1–10, 2015.
[5] A. Najafi, R. Golestanian. Simple swimmer at low reynolds number : Three linked spheres. Phys. Rev. E, 69, 062901, 2004. doi :10.1103/PhysRevE.69.062901.
May 5th, 2022
Jeannette Yen
Georgia Institute of Technology (USA)
Small-scale biological-physical-chemical interactions in the plankton:
Wake signatures formed by prey, predators, mates, schoolmates at intermediate Re regimes
Fascinating studies of terrestrial locomotion by kangaroos, lizards and crabs, flight by bats, birds, and insects, and propulsion by fish, frogs, and flagellated organisms have stirred the imagination of biologists and provoked the curiosity of physical scientists. In response, we have engaged biological oceanographers and fluid dynamic engineers to perform similar studies of plankton. Plankton are aquatic organisms that form the base of the aquatic food web and therefore, aquatic ecosystem balance depends on their survival. The term plankton is derived from the Greek word πλανκτος ("planktos"), meaning "wanderer" or "drifter". From quantitative analyses of three-dimensional trajectories, propulsion and morphology, and small-scale turbulence, we learn that plankton often do not go with the flow. Plankton operate at intermediate Reynolds numbers, generating watery signals that can be attenuated by viscosity and confused with small-scale turbulence. Yet messages are created, transmitted, perceived and recognized. These messages guide essential survival tasks of aquatic organisms. At the small-scale where biologically-generated behavior differs from physically-derived flow, we find plankton self-propel themselves, are aware of each other, and evolve in response to the fluid environment in surprising ways.
Apr 7th, 2022.
Kevin Du Clos
U. Oregon (USA)
Unsteady sinking behavior in diatoms
Diatoms are a diverse and ubiquitous group of marine phytoplankton. They are encased in a silicate shell, making them more dense than seawater; their sinking is responsible for up to 40% of particulate organic carbon export in the ocean. Diatoms are not passive sinkers, however; they regulate their sinking speeds in response to their own biological states and to environmental factors, such as irradiance and nutrient concentrations. Video-based techniques enable the tracking of individual sinking cells, providing insights into how diatoms regulate sinking speeds over multiple time scales, including an unsteady sinking behavior in which diatoms oscillate sinking speeds within seconds. I will present results on the factors affecting the steady and unsteady sinking behavior of the centric diatom Coscinodiscus wailesii and some recent insights into sinking in other diatom taxa.
March 3rd, 2022.
Arezoo Ardekani
Purdue U. (USA)
Hydrodynamics-mediated trapping of microbes
The interaction of motile microorganisms and surrounding fluids is of importance in a variety of biological and environmental phenomena including the formation of marine algal blooms and bacterial bioremediation. Many microorganisms, especially bacteria, actively search for nutrients via a process called chemotaxis. The physical constraints posed by hydrodynamics in the locomotion of microorganisms can combine with their chemotactic ability to significantly affect functions like colonization of nutrient sources and their patchiness. Motivated by bacterial bioremediation of hydrocarbons released during oil spills, I will discuss the role of hydrodynamics toward dictating distribution of microbes around interfaces and drops in the presence and absence of surfactant. I will also discuss the role of density stratification on swimming and settling dynamics. Density stratification hampers the vertical flow and substantially affects the sedimentation, the hydrodynamic interactions between a pair, and the collective behavior of suspensions in various ways depending on the relative magnitude of stratification, inertia (advection), and viscous (diffusion) effects. We show that a swimmer can experience change of stability based on the relative importance of the above-mentioned effects.
Feb 2nd, 2022..
Oscar Guadayol
U. Lincoln (UK)
An engineering tool for a phytoplankton cell
Viscosity is critically important to planktonic life, as it affects both the rate of diffusion of molecules and the motility of microbes. And yet, it is a property that has been traditionally neglected by physical oceanography because water viscosity is well constrained by temperature, salinity and pressure. We know, however, that exopolymeric substances (EPS) released by marine organisms can alter the bulk viscosity of seawater at large scales. The role of EPS in physically structuring the microscale environment remains hypothetical. We used microrheological techniques to map viscosity with micron resolution around phytoplankton cells and inside aggregates, revealing the existence of steep gradients at the microscale. These gradients, as our numerical models show, can alter the dynamics and spatial structure of the chemical landscape and affect the motility and chemotactic performance of bacteria. Altogether this suggests that secreting EPS could be a good strategy for a phytoplankton cell to scaffold the phycosphere and optimize both resource acquisition and interactions with bacteria.
December 8th, 2021
Douglas Brumley
University of Melbourne
The role of bacterial chemotaxis in marine nutrient cycling and symbioses
Bacterial motility, symbioses, and marine nutrient cycling unfold at the scale of individual microorganisms, and are inherently dynamic. Moreover, microorganisms are routinely exposed to microscopic fluid flows, which have the capacity to influence motility and redistribute chemical cues. In this talk, I will outline how combining video-microscopy, image processing and mathematical modelling can resolve dynamic microscale processes which underpin the ecology of microorganisms. I will also demonstrate how the highly-resolved processes at the scale of individual cells can be connected to bulk measurements at the population-level.
October 7th, 2021
Julia Schwartzman
Parsons Laboratory
Department of Civil and Environmental Engineering
MIT
Cellular division of labor in self-organized collectives supports decomposition by a marine bacterium
The physical form life takes, from single cells to multicellular organisms, is central to its function. Self-organization, the process through which order emerges in biological systems from local interactions, underlies an astonishing array of complex biological functions ranging from resource partitioning to environmental resilience to reproduction. In this talk, I will discuss how self-organization scaffolds a cellular division of labor in clonal collectives of a polysaccharide-degrading marine bacterium. I will present experiments and simulations supporting the ideas that cell-density dependent cooperation and competition cue phenotypic specialization within clonal collectives, that interaction of cell types leads to the self-organization of clonal collectives into structurally complex forms, and that this emergent structure scaffolds a division of labor that supports cycles of growth and dispersal.
September 21st, 2021
Anders Andersen
Centre for Ocean Life
National Institute of Aquatic Resources
Technical University of Denmark
Feeding flow and membranelle filtration in ciliates
Ciliates are ubiquitous in the marine environment and important consumers of phytoplankton and flagellates. The feeding in ciliates is complex and relies in many species on coordinated motion in bands of transversal rows of cilia known as membranelles. We explore the feeding in the ciliate Euplotes vannus that uses a single membranelle band to both generate feeding flow, retain food particles, and transport them to the mouth region. To obtain a mechanistic understanding of the feeding, we use high-speed video-microscopy. The cilia move parallel to the membranelle band towards the mouth region in the power strokes, and a metachronal wave propagates away from the mouth region parallel to the band and outwards along the membranelles. From the inside of the band, a gap therefore opens between neighboring membranelles, and while food particles are retained, water is drawn in and pushed across the membranelle band as the gap closes from the inside. We rationalize our findings in a model that compares favorably with our observations of clearance rate and membranelle motion.
This is joint work with Mads Rode and Thomas Kiørboe.
May 13th, 2021
Knut Drescher
Biozentrum
Universität Basel
Triggers and mechanisms of biofilm dispersal of Vibrio cholerae
Bacteria can generate benefits for themselves and their kin by living in multicellular, matrix-enclosed communities, termed biofilms. The decision-making strategies used by bacteria to weigh the costs between remaining in a biofilm or actively dispersing are largely unclear, even though the dispersal transition is a central aspect of the biofilm life cycle. Using a highly controlled flow system for biofilm cultivation and environmental control, I will first demonstrate our understand of the signals that trigger Vibrio cholerae biofilm dispersal, before showing how exactly cells actively disperse from the biofilm matrix.
April 8th, 2021
Nawish Wadhwa
Harvard University
The bacterial flagellar engine has an automatic gearshift
Motility is critical for the survival and dispersal of bacteria, and it plays an important role during infection. Regulation of bacterial motility via chemotaxis and gene regulation is well studied. However, recent work has added a new dimension to this problem. The flagellar motor of bacteria autonomously assembles and disassembles torque-generating stator units in response to changes in the external viscous load. In Escherichia coli, up to 11 stator units drive the motor at high load while all the stator units are released at low load. We study this process by artificially manipulating the motor load using electrorotation, where a high frequency rotating electric field applies an external torque on the flagellar motor (1). Using this technique, we can increase or decrease the motor load at will and measure the resulting stator remodeling. We measured stator remodeling in both clockwise and counterclockwise rotating motors, and found that the motor’s response has a conserved torque dependence (2). We built a model that captures the observed dynamics and provides insight into the underlying molecular interactions. Torque-dependent stator remodeling takes place within tens of seconds, making it a highly responsive autonomous control mechanism.
1. Wadhwa, N., Phillips, R., & Berg, H. C. (2019). Torque-dependent remodeling of the bacterial flagellar motor. PNAS, 116(24), 11764-11769.
2. Wadhwa, N., Tu, Y., & Berg, H. C. (2021). Mechanosensitive remodeling of the bacterial flagellar motor is independent of direction of rotation. PNAS, 118(15) e2024608118.
March 22, 2021
Yuval Jacobi
The Division of Environmental, Water and Agricultural Engineering, Technion – Israel Institute of Technology
and
School of Marine Sciences, Ruppin Academic Center
Evasive microalgae: surface interaction in suspension feeding by ascidians
Ascidians are benthic suspension feeders that feed by filtering seawater using a mucous filter. In the past, the efficiency and rate of particle capture by ascidians was considered to be governed by particle size and the pore size of the mucous filter. By measuring the particle capture efficiency of several ascidian species, in-situ, we found that ultraplankton cells (bacteria and microalgae sized 0.2-10 µm) are captured at a significantly lower efficiency compared with similar sized polystyrene microspheres (0.3-10 µm). This phenomenon was observed both with particles and microbes that are smaller than the proposed pore size of the ascidian filter and, surprisingly, also for particles that are larger than the proposed pore size. In addition, we found that altering the surface properties of polystyrene microspheres by coating them with long-chain nonionic surfactants can lead to a reduction in capture efficiency, if the size of the surfactant’s hydrophilic chain is between 280 Da and 12 kDa.
Using particle-tracking confocal microscopy, we measured the Brownian motion of polystyrene particles embedded in fresh mucus harvested from the ascidian Herdmania momus. Results indicate that the mobility of equal-sized particles, possessing different surface properties, correlates well with their capture efficiency by H. momus. This finding serves as direct evidence of the role played by surface interactions in determining particle capture by ascidians. Images of the ascidian mucus, obtained via cryogenic scanning electron microscopy, combined with the fact that large microbes (larger than the estimated pore size) are not always captured at 100% efficiency, suggest that the structure of the ascidian mucous filter may be different from the rectangular mesh previously suggested. Our results show that surface interactions have an important role in mucus-based suspension feeding. Furthermore, given the lack of a known particle selection mechanism in ascidians, we propose that some microbial plankton possess surface traits that increase their mobility inside the mucous filter. This mobility enables the crossing of some cells to the down-stream side of the filter and out to sea, and thus serves as a strategy for evading predation.
February 11th, 2021
Mimi Koehl
Department of Integrative Biology
University of California, Berkeley
Locomoting in a turbulent environment: Ways to study microscale processes in a large-scale ocean
A major challenge in studying ocean biophysics is integrating the different scales at which various physical and biological processes occur. How can we make large-scale field measurements and models that include the behaviors and physical features of real organisms? Conversely, how can we design small-scale experiments to measure those biological factors under hydrodynamic conditions that reflect what the organisms actually experience in the large-scale ocean? I will discuss examples of some of the approaches we have used to span different scales in our studies of how microscopic animals locomote in turbulent ambient water flow. We have been using the microscopic larvae of bottom-dwelling marine animals to explore how the interaction between the swimming or crawling by an organism and the turbulent water flow around them determines how they move through the environment.
