Roman Stocker, Ph.D.

Using microfluidics as a tool to mimic and manipulate a microbe's environment to understand their role in ocean's health


Research that focuses on microscale biophysical processes in the ocean and developing and applying visualization techniques at high spatial and temporal resolution to understand how microbes work.

Roman Stocker, Ph.D.

Research Description

I spy on the lives of microbes. My research focuses on microscale biophysical processes in the ocean and I enjoy developing and applying visualization techniques at high spatial and temporal resolution to understand how microbes work. Seeing is believing, but seeing microbes in action is challenging because of the minuscule size of their world. By using powerful microscopes, fast digital cameras, and advanced image analysis, we look at how microbes behave and interact in the context of ubiquitous physical processes (like turbulence and diffusion), the chemical environment (for example nutrients and oxygen) and the ecological landscape (their conspecifics, their predators and their viruses).

I am partial to motility. I find it fascinating that organisms 100-fold thinner than a human hair have motors and propulsion appendages and can swim at speeds equal to hundreds of their body lengths in each second! Microbes couple motility with sensing and are exquisitely able to measure concentrations in their environment. This allows them to search for nutrients, escape toxins, aggregate with each other, jump on particles and oil droplets, seek and infect corals. By understanding how they move, we can begin to understand the how, and the why, of many of these processes.

I am an engineer and love technology. My team, which mixes engineers with biologists and physicists, designs and builds microfluidic devices to improve our ability to study microbes. With microfluidics, we can interrogate the behaviors and functions of microbes with much greater flexibility, as we can mimic in the controlled conditions of the laboratory the microenvironments they experience in the ocean. With our collaborators, we also take these microdevices out to sea, in order to directly sample microbes based on their chemical preferences, and to begin to identify what microbes perform which functions at the actual (micro)scale at which the lives of these organisms unfold.

I enjoy integrating experimental observations with mathematical analysis. From the analysis of images, to the mathematical modeling of fluid flow and organism motility, math plays a crucial role in making our studies quantitative. I believe this to be important in assessing the actual effects of microbial processes and in meaningfully incorporating these processes in large-scale models of one of the most important ecosystems on our planet, the oceans.

Research Impact

My research is contributing to our understanding of the mechanisms of multiple microscale marine processes, which cumulatively determine how the ocean works at the ecosystem scale. My group has worked on motility and chemotaxis of marine bacteria and their unique locomotion system, on phytoplankton patchiness, on the chemical ecology and fluid dynamics of corals, on the ocean’s biological pump, on marine snow degradation, on the consequences of turbulence and density stratification on marine plankton, on microbial oil degradation in the sea, on the mechanisms underpinning bacterial diversity, and on the effects of fluid flow on surface biofouling.

In all these cases, we have employed a combination of direct observation in the laboratory, mathematical modeling and sometimes field experiments, to shed new light on fundamental mechanisms. For example, we have shown that ocean currents and turbulence can be important in determining the spatial distribution of phytoplankton, forming small-scale patches as well as extensive thin layers frequently observed by oceanographers in coastal waters. We have identified motility and chemotaxis as important behaviors for bacterial pathogens to locate and reach the surface of their coral hosts. Our microfluidic visualization has revealed how marine bacteria can exploit the plumes of ‘marine snow’ particles, the drivers of the vertical carbon flux in the ocean, and how the microbial degradation kinetics of these particles are highly non-linear. We have imaged the degradation of crude oil at the single-oil-droplet level, proposing a new model for oil degradation in the sea. And we have begun to apply microfluidics in oceanographic deployments and to pursue the incredibly promising handshake between microfluidic technology and omics. A theme of strong current interest in my group is the role on bacterial growth and behavior of fast (minute-timescale) environmental fluctuations, such as those typically encountered by marine microbes in regards to nutrient availability resulting from turbulence and microscale patchiness. Our goal in this project if to determine how the ubiquitous fluctuations in the sea must be factored into the routinely ‘bulk’ approaches in microbial oceanography.

Media Press

MIT News- Nature's tiny engineers

Wired, U.K. - The day-to-day life of a coral reef, visualised

The New York Times - Behind Red Tides, the Swimming and Shape of Plankton

The New York Times - For Cats, a Big Gulp With a Touch of the Tongue

MIT News - In Profile: Roman Stocker finds big effects from tiny organisms


related links

Marine Microbiology Initiative Science Massachusetts Institute of Technology, Office of Sponsored Programs Back


Ph.D., Civil and Environmental Engineering
University of Padova, Italy, 2002

B. Eng., Civil Engineering
University of Padova, Italy, 1998


Maseeh Award for Teaching, Massachusetts Institute of Technology, 2012

Milton Van Dyke Award from Division of Fluid Dynamics, American Physical Society, 2011

ASLO Lindeman Award for outstanding paper in aquatic sciences under age 35, 2010

Doherty Professorship of Ocean Utilization, 2007 – 2009


Shapiro, O. H., V. I. Fernandez, M. Garren, J. S. Guasto, F. P. Debaillon-Vesque, E. Kramarsky-Winter, A. Vardi, & R. Stocker. (2014). Vortical ciliary flows actively enhance mass transport in reef corals. Proc Natl Acad Sci U S Adoi: 10.1073/pnas.1323094111

Yawata, Y., O. X. Cordero, F. Menolascina, J. H. Hehemann, M. F. Polz, & R. Stocker. (2014). Competition–dispersal tradeoff ecologically differentiates recently speciated marine bacterioplankton populations. Proc Natl Acad Sci U S A, 111(15), 5622-5627. doi: 10.1073/pnas.1318943111

Rusconi, R. , Jeffrey S. Guasto, & R. Stocker. (2014). Bacterial transport suppressed by fluid shear. Nat Physdoi: 10.1038/nphys2883

Kashtan, N., S. E. Roggensack, S. Rodrigue, J. W. Thompson, S. J. Biller, A. Coe, H. Ding, P. Marttinen, R. R. Malmstrom, R. Stocker, M. J. Follows, R. Stepanauskas, & S. W. Chisholm. (2014). Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus. Science, 344(6182), 416-420. doi: 10.1126/science.1248575

Garren, M., K. Son, J. B. Raina, R. Rusconi, F. Menolascina, O. H. Shapiro, J. Tout, D. G. Bourne, J. R. Seymour, & R. Stocker. (2014). A bacterial pathogen uses dimethylsulfoniopropionate as a cue to target heat-stressed corals. ISME J, 8(5), 999-1007. doi: 10.1038/ismej.2013.210

Son, Kwangmin, Jeffrey S. Guasto, & Roman Stocker. (2013). Bacteria can exploit a flagellar buckling instability to change direction. Nature Physicsdoi: 10.1038/nphys2676

Affiliated Investigators