Methods for characterizing the co-development of biofilm and habitat heterogeneity

Xiaobao Li*, Jisun L. Song, Alessandro Culotti, Wei Zhang, David L. Chopp, Nanxi Lu, Aaron I. Packman

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


Biofilms are surface-attached microbial communities that have complex structures and produce significant spatial heterogeneities. Biofilm development is strongly regulated by the surrounding flow and nutritional environment. Biofilm growth also increases the heterogeneity of the local microenvironment by generating complex flow fields and solute transport patterns. To investigate the development of heterogeneity in biofilms and interactions between biofilms and their local micro-habitat, we grew mono-species biofilms of Pseudomonas aeruginosa and dual-species biofilms of P. aeruginosa and Escherichia coli under nutritional gradients in a microfluidic flow cell. We provide detailed protocols for creating nutrient gradients within the flow cell and for growing and visualizing biofilm development under these conditions. We also present protocols for a series of optical methods to quantify spatial patterns in biofilm structure, flow distributions over biofilms, and mass transport around and within biofilm colonies. These methods support comprehensive investigations of the co-development of biofilm and habitat heterogeneity.

Original languageEnglish (US)
Article numbere52602
JournalJournal of Visualized Experiments
Issue number97
StatePublished - Mar 11 2015


  • Bioengineering
  • Biofilm development
  • Chemical gradient
  • Flow characterization
  • Fluorescent tracer
  • Issue 97
  • Microfluidic flow cell
  • Particle tracking
  • Solute transport

ASJC Scopus subject areas

  • Neuroscience(all)
  • Chemical Engineering(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

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