Prof. Roman Stocker

PI | ETH Zurich |


Much of the research of the Stocker lab is centered on bacterial motility and chemotaxis and the interaction of these behaviors with fluid flow. Using microfluidics, advanced microscopy and image analysis, in combination with mathematical modeling, we seek to understand how fluid dynamics and behavior interact to shape the ecology of aquatic microbes and govern their contribution to global biochemical cycles. Our recent work has demonstrated the value of using optimal foraging theory to understand the behavior of bacteria as they exploit and disperse among marine particles, and shown that sinking enhances the degradation of marine particles by bacteria. We have also developed a series of novel microfluidics-based platforms to facilitate the analysis of microbial ecology, including a platform that allows automated Raman-activated sorting of microbial cells according to their ecological functions, and an in situ chemotaxis assay to study the behavior of aquatic microbial communities in the field.

Selected Publications:

Nguyen J., Lara-Gutiérrez J. and Stocker R., 2020, “Environmental fluctuations and their effects on microbial communities, populations, and individuals”, FEMS Microbiology Reviews, doi:10.1093/femsre/fuaa068.

Lee K.S., Pereira F.C., Palatinszky M., Behrendt L., Alcolombri U., Berry D., Wagner M. and Stocker R., 2020, “Optofluidic Raman-activated cell sorting for targeted genome retrieval or cultivation of microbial cells with specific functions”, Nature Protocols, doi:10.1038/s41596-020-00427-8.

Gralka M., Szabo R., Stocker R. and Cordero O.X., 2020, “Trophic interactions and the drivers of microbial community assembly”, Current Biology, 30, R1176-R1188.

Yawata Y., Carrara F., Menolascina F. and Stocker R., 2020, “Constrained optimal foraging by marine bacterioplankton on particulate organic matter”, PNAS, 117, 25571-25579.

Behrendt L., Salek M.M., Trampe E.L., Fernandez V.I., Lee K.S., Kühl M. and Stocker R., 2020, “PhenoChip: A single-cell phenomic platform for high-throughput photophysiological analyses of microalgae”, Science Advances, 6, 2754.

Brumley D.R., Carrara F., Hein A.M., Hagstrom G.I., Levin S.A. and Stocker R., 2020, “Cutting through the noise: bacterial chemotaxis in marine microenvironments”, Frontiers in Marine Science, 7, 527.

Slomka J. and Stocker R., 2020, “Bursts characterize coagulation of rods in a quiescent fluid”, Physical Review Letters, 124, 25-26.

Secchi E., Vitale A., Miño G.L., Kantsler V., Eberl L., Rusconi R. and Stocker R., 2020, “The effect of flow on swimming bacteria controls the initial colonisation of curved surfaces”, Nature Communications, 11, 2851.

Gao C., Fernandez V.I., Lee K.S., Fenizia S., Pohnert G., Seymour J.R., Raina J.B. and Stocker R., 2020, “Single-cell bacterial transcription measurements reveal the importance of dimethylsulfoniopropionate (DMSP) hotspots in ocean sulfur cycling”, Nature Communications, 11, 1942.

Slomka J., Alcolombri U., Secchi E., Stocker R. and Fernandez V.I., 2020, “Encounter rates between bacteria and small sinking particles”, New Journal of Physics, 22, 043016.

Lee K.S., Wagner M. and Stocker R., 2020, “Raman-based sorting of microbial cells to link functions to their genes”, Microbial Cell, 7, 62-65.
Slomka J. and Stocker R., 2020, “On the collision of rods in a quiescent fluid”, PNAS, 117, 3372-3374.

Lovecchio S., Climent E., Stocker R. and Durham W.M., 2019, “Chain formation can enhance the vertical migration of phytoplankton through turbulence”, Science Advances, 5, eaaw7879.

Wheeler J.D., Secchi E., Rusconi R. and Stocker R., 2019, “Not just going with the flow: the effects of fluid flow on bacteria and plankton”, Annual Review of Cell and Developmental Biology, 35, 213-237.

Salek M.M., Carrara F., Fernandez V.I. and Stocker R., 2019, “Bacterial maze runners reveal hidden diversity in chemotactic performance”, Microbial Cell, 6, 370-372.

Zaoli S., Giometto A., Maranon E., Escrig S., Meibom A., Ahluwalia A., Stocker R., Maritan A. and Rinaldo A., 2019, “Generalized size scaling of metabolic rates based on single-cell measurements with freshwater phytoplankton”, PNAS, 116, 17323-17329.

Brumley D.R., Carrara F., Hein A.M., Yawata Y., Levin S.A. and Stocker R., 2019, “Bacteria push the limits of chemotactic precision to navigate dynamic chemical gradients”, PNAS, 116, 10792-10797.

Salek M.M., Carrara F., Fernandez V.I., Guasto J.S. and Stocker R., 2019, “Bacterial chemotaxis in a microfluidic T-maze reveals strong phenotypic heterogeneity in chemotactic sensitivity”, Nature Communications, 10, 1877.

Raina J.B., Fernandez V.I., Lambert B., Stocker R. and Seymour J.R., 2019, “The role of microbial motility and chemotaxis in symbiosis”, Nature Reviews Microbiology, 17, 284-294.

Fernandez V.I., Yawata Y. and Stocker R., 2019, “A foraging mandala for aquatic microorganisms”, ISME Journal, 13, 563-575.

Research Interests

Bacterial motility, Chemotaxis, Microfluidics, Microscopy, Modeling

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Prof. Roman Stocker