title: Methods for characterizing the co-development of biofilm and habitat heterogeneity.
abstract: 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.
authors: Department of Civil and Environmental Engineering, Northwestern University; lixiaobao1401@gmail.com.
authors: Xiaobao
authors: X
authors: Li
authors: Department of Chemical and Biological Engineeering, Northwestern University.
authors: Jisun L
authors: JL
authors: Song
authors: Department of Civil and Environmental Engineering, Northwestern University.
authors: Alessandro
authors: A
authors: Culotti
authors: Department of Civil and Environmental Engineering, Northwestern University.
authors: Wei
authors: W
authors: Zhang
authors: Department of Applied Mathematics and Engineering Sciences, Northwestern University.
authors: David L
authors: DL
authors: Chopp
authors: Department of Civil and Environmental Engineering, Northwestern University.
authors: Nanxi
authors: N
authors: Lu
authors: Department of Civil and Environmental Engineering, Northwestern University.
authors: Aaron I
authors: AI
authors: Packman
mesh_terms: D018441:Biofilms / Q000254:growth & development*; D017753:Ecosystem; D004926:Escherichia coli / Q000502:physiology*; D044085:Microfluidics / Q000295:instrumentation / Q000379:methods; D018613:Microscopy, Confocal / Q000379:methods; D011550:Pseudomonas aeruginosa / Q000502:physiology*