Generating controlled, dynamic chemical landscapes to study microbial behavior

Francesco Carrara, Douglas R. Brumley, Andrew M. Hein, Yutaka Yawata, M. Mehdi Salek, Kang Soo Lee, Elzbieta Sliwerska, Simon A. Levin, Roman Stocker

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


We demonstrate a method for the generation of controlled, dynamic chemical pulses―where localized chemoattractant becomes suddenly available at the microscale―to create micro-environments for microbial chemotaxis experiments. To create chemical pulses, we developed a system to introduce amino acid sources near-instantaneously by photolysis of caged amino acids within a polydimethylsiloxane (PDMS) microfluidic chamber containing a bacterial suspension. We applied this method to the chemotactic bacterium, Vibrio ordalii, which can actively climb these dynamic chemical gradients while being tracked by video microscopy. Amino acids, rendered biologically inert ('caged') by chemical modification with a photoremovable protecting group, are uniformly present in the suspension but not available for consumption until their sudden release, which occurs at user-defined points in time and space by means of a near-UV-A focused LED beam. The number of molecules released in the pulse can be determined by a calibration relationship between exposure time and uncaging fraction, where the absorption spectrum after photolysis is characterized by using UV-Vis spectroscopy. A nanoporous polycarbonate (PCTE) membrane can be integrated into the microfluidic device to allow the continuous removal by flow of the uncaged compounds and the spent media. A strong, irreversible bond between the PCTE membrane and the PDMS microfluidic structure is achieved by coating the membrane with a solution of 3-aminopropyltriethoxysilane (APTES) followed by plasma activation of the surfaces to be bonded. A computer-controlled system can generate user-defined sequences of pulses at different locations and with different intensities, so as to create resource landscapes with prescribed spatial and temporal variability. In each chemical landscape, the dynamics of bacterial movement at the individual scale and their accumulation at the population level can be obtained, thereby allowing the quantification of chemotactic performance and its effects on bacterial aggregations in ecologically relevant environments.

Original languageEnglish (US)
Article numbere60589
JournalJournal of Visualized Experiments
Issue number155
StatePublished - Jan 2019

All Science Journal Classification (ASJC) codes

  • General Chemical Engineering
  • General Immunology and Microbiology
  • General Biochemistry, Genetics and Molecular Biology
  • General Neuroscience


  • Bioengineering
  • Caged compounds
  • Chemical pulses
  • Chemotaxis
  • Issue 155
  • Microbial ecology
  • Microfluidics
  • Motility
  • Photolysis
  • Polycarbonate membrane


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