Phytoplankton in flow

Phytoplankton are photosynthetic microorganisms that form the base of most aquatic food webs and are responsible for half of global photosynthesis. Many species swim using flexible flagella and can reach remarkable speeds (up to 50 bodylengths/s) in relation to their small size (often 5-50 microns). Motility has many consequences within an ocean that is itself in constant motion. For example, using a combination of millifluidic experiments and mathematical modeling, we have shown that phytoplankton motility (biased by velocity gradients in the ambient water through a process called gyrotaxis) can explain the occurrence of the dramatic thin layers of high phytoplankton concentration that are often observed in the ocean and thought to be precursors of red tides. We also discovered that the velocity gradients that characterize ocean turbulence at the smallest scales can result in strong microscale patchiness in the distribution of phytoplankton, depending on their swimming speed and stability. Coupling of shape and flow could also change light climate in the ocean by increasing the optical backscattering of natural plankton assemblages, through the preferential alignment of elongated plankton induced by fluid shear. However, despite their small size, phytoplankton are not passively at the mercy of fluid flow. Recently we have found that phytoplankton display an active behavioral response to turbulence-like cues associated with the smallest turbulent eddies in the ocean, whereby a subtle change in morphology triggers a shift in the direction of migration among phytoplankton that commute vertically across the water column. We are now learning more about the behavioral and adaptive strategies of phytoplankton in the face of turbulence through scaled up experiments in a turbulence tank, together with single-cell tracking and molecular techniques like transcriptomics.

For more information, contact: Anupam Sengupta (, Francesco Carrara (, Jeanette Wheeler ( or Ulrike Pfreundt (

Bacteria in flow: Unexpected interactions

Functional traits are attributes that influence the fitness of a species. We use microfluidic experiments, microscale visualization and mathematical modeling to study the interplay between bacterial functional traits, such as shape and motility, and flow, which is ubiquitous in bacterial habitats. For example, bacterial flagella are chiral (specifically: helical).

We discovered that the coupling of chirality and shear leads to a preferentially oriented movement, bacterial rheotaxis, akin to that in fish but of a passive nature. Bacterial rheotaxis is characterized by a drift across streamlines that originates from the reorientation of the cell body due to a lift force acting on the chiral flagellum and could hamper the quest of nutrients by bacteria. We are currently performing extensive microfluidic experiments to better understand the rich interactions among bacterial motility and flow.

Now working on this theme: Roberto Rusconi, Jeff Guasto.

The mechanics of bacterial flagella: Buckling at the nanoscale

Micron-sized bacteria represent the smallest and most abundant life form on Earth. Strikingly, bacteria are motile despite their small size and understanding their swimming mechanics is both intriguing and important. Although bacterial motility has been studied for half a century, we recently discovered a new mechanism of reorientation, used broadly among marine bacteria, which all (95% of swimming species) have only a single flagellum, in contrast for example to E. coli. By combining video microscopy at up to 2000 frames/s, image analysis, and mechanical stability theory, we visualized the dynamics of the cell and its flagellum as it changes swimming direction and discovered that the mechanism that allows them to reorient is a buckling instability of their flagellum. This project revealed an unexpected role of flexibility in the locomotion of prokaryotes, whose flagella are typically assumed to be rigid. Intriguingly, it shows how structural failure can be turned into biological function, a dramatic and elegant adaptation by the smallest organisms on the planet.

Now working on this theme: Kwangmin Son, Jeff Guasto.

Coral ecology and disease: A microscale perspective

Tropical reef-building corals are complex biological systems comprised of a delicate balance of symbioses among the coral animal, intracellular dinoflagellates (zooxanthellae), bacteria, archaea, and viruses. We use microfluidic experiments and video microscopy to tease apart the chemical and physical interactions underpinning coral health and disease processes at the microscale. We study these processes both in the laboratory and in field settings, recently on Heron Island (Great Barrier Reef). We are currently focused on examining (i) pathogen behaviors and their response to host-derived chemical cues, and how this interaction is affected by increases in seawater temperature; and (ii) the complex ciliary flows that the coral animal creates along its surface and how it affects mass transport to and from the coral, in particular the export of oxygen from the zooxathellar photosynthesis.

Now working on this theme: Melissa Garren, Orr Shapiro, Vicente Fernandez, Kwangmin Son, Roberto Rusconi, Theresa Santiano-McHatton.

Microscale microbial hotspots in the ocean: Bacteria in the phycosphere

Chemotaxis enables marine bacteria to utilize microscale nutrient patches and many marine bacteria are excellent at chemotaxis, markedly outperforming the classic chemotaxis model organism E. coli. In naturally occurring bacterial communities, we have observed the dramatic, fast formation of ephemeral accumulations of bacteria by chemotaxis into the ‘phycosphere’, the microscale region surrounding individual phytoplankton cells. Using high-resolution video microscopy and cell tracking, we have for the first time precisely dissected the spatio-temporal dynamics of this process. We are using this unique data set as input for a mathematical model that ‘scales up’ these microscale dynamics to yield predictions of the relative contribution of motile and non-motile bacteria to the utilization of nutrients from the phycosphere. By merging direct observations with ecological modeling, these results will help us understand resource competition among diverse bacterial communities and the roles of phytoplankton-bacteria interactions in biogeochemical cycling.

Now working on this theme: Steven Smriga, Vicente Fernandez.

Fertilization in the sea: Sperm sensing and biomechanics

Motility enables sperm cells (~50 microns long) to deliver their genetic cargo to egg cells for fertilization, a key step in the reproductive process for a host of organisms including mammals (especially humans) and external fertilizers (e.g. marine invertebrates).

Similarly to many other motile single cells, sperm are guided by chemical gradients, but rather than seeking out nutrients, sperm are guided by egg-generated chemical signals. Complicating this process is the ubiquitous presence of fluid flow, be it from ocean turbulence for marine organisms or from ciliary-driven flows in the human reproductive tract. We are currently working to unravel the complex interactions between sperm and their physicochemical environment, specifically how sperm sense and respond to chemical gradients and how the flagellar biomechanics of sperm swimming are affected by external fluid flow. To accomplish this, we use a suite of novel microfluidic devices to control both chemical and hydrodynamic gradients and study the motility of sperm from a range of model systems including humans and various species of sea urchisn, through high-speed video microscopy and cell tracking.

Now working on this theme: Jeff Guasto, Gabriel Juarez, Mehdi Salek.

Bacterial turbulence: Collective behavior at the microscale

While bacteria often occur in dilute suspensions, in some cases these suspensions can be very dense. When this occurs, bacteria exhibit correlated dynamics on spatial scales much larger than an individual bacterium and generate flows faster than the individuals’ swimming speed. The resulting flows, visually similar to turbulence, can increase mixing and decrease viscosity. Using a new design of microfluidic devices, we study suspensions of Bacillus subtilis under carefully controlled oxygen gradients, to assess the interplay between the coherent large-scale motions of the suspension, oxygen transport, and the directional response of cells to oxygen gradients (aerotaxis).

Now working on this theme: Vicente Fernandez, Roberto Rusconi, Steven Smriga

Bacterial competition in turbulent waters

In the ocean, some bacteria swim and some do not. Who wins and when? To find out, we  developed a mathematical model of nutrient competition among bacteria in the ocean and implemented it within a Direct Numerical Simulation of turbulent flow, which takes into account the effect of turbulence on the transport and dispersion of nutrient patches and bacteria. We have found that (i) an optimal swimming speed guarantees the best advantage to swimmers and is broadly in agreement with observed swimming speeds, and (ii) an intermediate turbulence intensity optimally favors motility, because it creates chemical gradients and does not mix them away too rapidly. This approach is flexible, can include multiple other bacterial traits, and represents a promising new ecological framework to understand the evolution of different foraging strategies and the competition for nutrients among bacteria in the ocean

(Previously working on this topic: John Taylor).

Living at the oil-water interface: The biophysics of bacterial oil degradation

Approximately three million tons of crude oil find their way into the sea each year. In response to natural oil seeps occurring for millions of years, some marine microbes have evolved mechanisms to degrade oil, which they use as a carbon source for growth. Many species of oil-degrading bacteria are equipped with flagella that enable the cells to swim and actively pursue nutrient gradients in their local surroundings. We are interested in understanding and quantifying the link between motility at oil-water interfaces and how the encounter and attachment dynamics of microbes with oil influence oil degradation. We are characterizing the system at the microbe-oil droplet level using dedicated macro- and micro-fluidic devices and capturing the swimming behavior and attachment dynamics of individual bacteria near the interface with phase contrast and epifluorescent microscopy and image analysis. Quantifying the physical interaction of motile bacteria to liquid-liquid interfaces will promote a fundamental understanding of oil-microbe interactions in the ocean and potentially inform improved oil bioremediation strategies.

Now working on this theme: Gabriel Juarez, Steven Smriga, Vicente Fernandez

Bacterial chemotaxis: Signal integration and adaptation

Chemotaxis, the ability of cells to detect and respond to a gradient in chemical concentration, plays a central role in microbial ecology. We develop new microfluidic approaches to create carefully controlled, spatial and temporal gradients of (single or multiple) chemical stimuli. We use these to study the motility and growth response of bacteria to transient stimuli, sensory adaptation, the integration of different signals, and the role of metabolism on chemotaxis (energytaxis).

Now working on this theme: Vicente Fernandez, Filippo Menolascina, Kwangmin Son, Yutaka Yawata (previously: Tanvir Ahmed).

Bacterial biofilms: Surface detachment and Quorum sensing

Bacteria often adhere to surfaces, where they develop polymer-encased communities (biofilms) that display dramatic resistance to antibiotic treatment. The permanence of biofilms on surfaces thus poses serious risks of infection by and transmission of pathogens, so that a better understanding of bacterial detachment from surfaces may lead to novel strategies for biofilm disruption and removal. Using micro-contact printing, we can produce carefully controlled biofilms by creating hydrophobic patches on glass substrates, which strongly favor bacterial attachment and on which biofilms rapidly develop. These controlled patches then allow us to study a number of biofilm processes, including (i) the detachment of cells due to passage of air plugs and (ii) how cell-to-cell communication (quorum sensing) in biofilms depends on the size of the biofilm and the strength of the ambient flow.

Now working on this theme: Hongchul Jang, Roberto Rusconi.

Microfluidic cell sorting

For many applications, it is desirable to not only be able to visualize microbes and their interactions, but subsequently sort and sample them for further analysis. We are working on approaches to sort microbes in a number of settings, including (i) a microfluidic module for the sorting of phytoplankton cells to attach to FlowCytobot, an underwater flow cytometer developed at WHOI by Rob Olson and Heidi Sosik; and (ii) a microfluidic chemotaxis device that enables sorting of microbes according to their chemotactic abilities and preferences.

Now working on this theme: Bennett Lambert, Steve Smriga, Mehdi Salek, Roberto Rusconi.

The effect of density stratification on marine microbes and particles

Peculiar fluid mechanics arise when the motion of a particle or the motility of a microbe are considered in the context of the density stratification that is widespread in the ocean, where it is caused by vertical temperature gradients (thermoclines) or salinity gradients (haloclines) . Through numerical simulations and laboratory experiments, we have found that density stratification can considerably increase the drag on small settling particles, and in particular of porous particles such as marine snow, and it can alter the spatial signature and energy consumption of swimming microorganisms (PRL, PNAS).

(Previously working on this topic: King Yeung Yick, Arezoo Ardekani, Kolia Kindler).