Advanced techniques for in situ analysis of the biofilm matrix (structure, composition, dynamics) by means of laser scanning microscopy

The extracellular constituents in bioaggregates and biofi lms can be imaged four dimensionally by usinglaser scanning microscopy. In this protocol we provide guidance on how to examine the various extracellularcompartments in between microbial cells and communities associated with interfaces. The currentoptions for fl uorescence staining of matrix compounds and extracellular microhabitats are presented.Furthermore, practical aspects are discussed and useful notes are added. The chapter ends with a briefintroduction to other approaches for EPS analysis and an outlook for future needs.