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Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering

6 ARTICLES PUBLISHED IN JoVE

Biology

Chemotactic Response of Marine Micro-Organisms to Micro-Scale Nutrient Layers

Justin R. Seymour¹, Marcos¹, Roman Stocker¹

¹Environmental Microfluidics Group, MIT - Massachusetts Institute of Technology

The fabrication of microfluidic channels and their implementation in experiments for studying the chemotactic foraging behaviour of marine microbes within a patchy nutrient seascape and the swimming behaviour of bacteria within shear flow are described.

Biology

Studies of Bacterial Chemotaxis Using Microfluidics - Interview

Roman Stocker¹

¹Environmental Microfluidics Group, MIT - Massachusetts Institute of Technology

Studies of Bacterial Chemotaxis Using Microfluidics - Interview

Bioengineering

Generating Controlled, Dynamic Chemical Landscapes to Study Microbial Behavior

Francesco Carrara¹, Douglas R. Brumley², Andrew M. Hein³, Yutaka Yawata^4,5, M. Mehdi Salek¹, Kang Soo Lee¹, Elzbieta Sliwerska¹, Simon A. Levin⁶, Roman Stocker¹

¹Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ²School of Mathematics and Statistics, University of Melbourne, ³Institute of Marine Sciences, University of California, Santa Cruz, ⁴Faculty of Life and Environmental Sciences, University of Tsukuba, ⁵Microbiology Research Center for Sustainability, University of Tsukuba, ⁶Department of Ecology and Evolutionary Biology, Princeton University

A protocol for the generation of dynamic chemical landscapes by photolysis within microfluidic and millifluidic setups is presented. This methodology is suitable to study diverse biological processes, including the motile behavior, nutrient uptake, or adaptation to chemicals of microorganisms, both at the single cell and population level.

Environment

In Situ Chemotaxis Assay to Examine Microbial Behavior in Aquatic Ecosystems

Estelle E. Clerc¹, Jean-Baptiste Raina², Bennett S. Lambert³, Justin Seymour², Roman Stocker¹

¹Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, ²Climate Change Cluster, University of Technology Sydney, ³School of Oceanography, University of Washington

Presented here is the protocol for an in situ chemotaxis assay, a recently developed microfluidic device that enables studies of microbial behavior directly in the environment.

Engineering

Patterning of Microorganisms and Microparticles through Sequential Capillarity-assisted Assembly

Roberto Pioli¹, Roman Stocker¹, Lucio Isa², Eleonora Secchi¹

¹Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, ²Department of Materials, ETH Zurich

We present a technology that uses capillarity-assisted assembly in a microfluidic platform to pattern micro-sized objects suspended in a liquid, such as bacteria and colloids, into prescribed arrays on a polydimethylsiloxane substrate.

Environment

A Microfluidic Platform to Study Bioclogging in Porous Media

Dorothee L. Kurz^1,2, Eleonora Secchi¹, Roman Stocker¹, Joaquin Jimenez-Martinez^1,2

¹Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, ²Department Water Resources and Drinking Water, Swiss Federal Institute of Aquatic Science and Technology

The present protocol describes a microfluidic platform to study biofilm development in quasi-2D porous media by combining high-resolution microscopy imaging with simultaneous pressure difference measurements. The platform quantifies the influence of pore size and fluid flow rates in porous media on bioclogging.