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Environmental Microfluidics at MIT

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The Fluid Mechanics of Plankton in the Coastal Ocean
Roman Stocker

December 2015


Thin layers of phytoplankton that form in the top 50 meters of the ocean are analogous to watering holes in a savanna - localized areas of concentrated resources that draw a wide range of organisms and thus play a disproportionate role in the ecological landscape. These layers of single-celled, photosynthetic organisms can be a few centimeters to several meters thick; span tens of kilometers horizontally; and last hours to weeks. When a toxic species of phytoplankton forms a thin layer, that layer can generate a harmful algal bloom - an explosion in the population of toxic phytoplankton that sickens or kills the larger animals that ingest the cells. Because these tiny creatures form the base of the marine food web and cumulatively produce half the world's oxygen, the thin layers have enormous ecological ramifications and can affect human activities, like fisheries and the tourism industry, in coastal zones worldwide. But until now, scientists knew little about the mechanisms responsible for their formation.


Roman Stocker of MIT's Department of Civil and Environmental Engineering studies environmental fluid mechanics at the microscale. His 'Environmental Microfluidics Group' focuses on the interplay of motile microorganisms and fluid flow by creating microhabitats and using video-microscopy to record the behavior and the fluid mechanics of plankton. In recent work, Stocker's team explored the connection between the movements of motile phytoplankton and formation of thin layers using experiments and mathematical modeling.


Stocker's group demonstrated that thin layers can form when the vertical migration of phytoplankton is disrupted by hydrodynamic shear generated by tidal currents, wind stress or internal waves. In their quest for sunlight, many phytoplankton exhibit a natural tendency to swim upwards towards the ocean's surface. However, Stocker's new findings show that this vertical motility can be thwarted in regions where the shear exceeds a critical value. Shear, in this case strong variations in horizontal water velocity, causes the cells to tumble end over end, trapping them at depth. As phytoplankton attempt to transverse a zone of enhanced shear on their daily commute to the morning light, they could be snared by the flow, confining the billions of cells to a region only a few tens of centimeters in depth. Using video-microscopy, Stocker's team tracked the movements of individual cells as they become trapped in the high-shear layer. They also used individual-based and continuum mathematical models to describe the movements of the swimming cells and proved that they cannot escape the layers until the shear decreases.


Blooms of harmful algae are a major source of social and economic concern, particularly near coastal areas, as they create billions of dollars in annual losses to fishing and recreational industries worldwide and they are occurring more frequently. The explanation by Stocker's team of how these common, startlingly dense layers of photosynthetic phytoplankton form, moves the scientific community a step closer to being able to predict harmful algal blooms. The work also opens a new direction in environmental fluid mechanics, by demonstrating that the coupling of fluid flow and biological processes can lead to new insights into environmental problems.

Selected Publications

Durham W.M., Kessler J.O. and Stocker R., 2009, "Disruption
of motility by shear triggers formation of thin phytoplankton
layers", Science, 323, 1067-1070.
Stocker R., Seymour J.R., Samadani A., Hunt D.E. & Polz M.,
2008, "Rapid chemotactic response enables marine bacteria
to exploit ephemeral microscale nutrient patches",
Proceedings of the National Academy of Sciences, 105, 4209-
Marcos, Fu H., Powers T. and Stocker R., 2009, "Separation of
microscale objects by flow", Physical Review Letters, 102,
Seymour J.R., Simó R., Ahmed T. and Stocker R., 2010,
"Chemoattraction to dimethyl- sulfoniopropionate
throughout the marine microbial food web", Science, 329,
Kindler K., Khalili A. and Stocker R., 2010,
"Diffusion-limited retention of porous
particles at density interfaces", Proceedings of
the National Academy of Sciences, 107, 22163-
Reis P.M., Jung S., Aristoff J.M. and Stocker R.,
2010, "How cats lap: water uptake by Felis
catus", Science, 330, 1231-1234 (all authors
equal in status).
Guasto J.S., Rusconi R. and Stocker R., 2012,
"Fluid mechanics of planktonic
microorganisms", Annual Review of Fluid
Mechanics, 44, 373-400.

Core Competencies

  • Biological fluid mechanics
  • Microfluidics
  • Microbial ecology
  • Low Reynolds number flows
  • Oceanography

Roman Stocker (photo M. Pilotto)

Current Research Team Members:
 Roman Stocker (PI)
 Michael Barry (Ph.D. Candidate)
 Kwangmin Son (Ph.D. Candidate)
 Hongchul Jang (Ph.D. Candidate)
 Roberto Rusconi (Postdoc)
 Jeffrey Guasto (Postdoc)
 Steven Smriga (Postdoc)
 Melissa Garren (Postdoc)
 Yutaka Yawata (Postdoc)
 Gabriel Juarez (Postdoc)
 Filippo Menolascina (Postdoc)
 Vicente Fernandez (Postdoc)

Recent Graduates and Postdocs:
 William Durham (Lecturer, U. Oxford)
 Justin Seymour (Lecturer, U.T. Sydney)
 John Taylor (Lecturer, U. Cambridge)

Current Research Collaborations:
 Viola Vogel (ETH)
 Mimi Koehl (UC Berkeley)
 Eduardo Sontag (Rutgers U.)
 Ray Goldstein (U. Cambridge)
 Eric Climent (IMFT, Toulouse, France)
 Richard Zimmer (UCLA)