Fundamentals of biofilm research

Introduction to biofilms and to biofilm research Introduction Terminology Characterizing selected parts of biofilm systems Characterizing microbial growth and biofilm formation Biofilm-based technologies Strategy of biofilm research Research program Interpreting results of biofilm studies Imaging and characterizing biofilm components Optical microscopy Fluorescence microscopy Electron microscopy Atomic force microscopy Microscopy for surface analysis Nuclear magnetic resonance imaging Laboratory biofilm reactors and their applications Introduction Variables in biofilm reactors LBRs as scale models Factors affecting biofilm processes in LBRs Operating modes of LBRs LBRs and their typical applications Using LBRs in conjunction with other tools to explore biofilm processes at the microscale Functionality of LBRs Sensors useful in biofilm research Fundamental concepts in electrochemistry and principles of electrochemical sensors Microsensors Microsensors: Construction, instrumentation, and calibration Introduction Constructing microelectrodes Constructing fiber optic microsensors Controlling microelectrode movements and data acquisition Quantifying biofilm structure The need to quantify biofilm structure Types of images Computing parameters from biofilm images Quantifying biomass distribution in 3-D from stacks of biofilm images Interfering effects Testing available software packages quantifying biofilm structure Directions of future research on quantifying biofilm structure Biofilms on metals and other electrically conductive surfaces Introduction Basic electrochemical concepts relevant to understanding the effects of biofilms on metals Abiotic corrosion of active metals: Iron Abiotic corrosion of passive metals Quantifying electron transfer processes in electrochemically active biofilms Electrochemical techniques for studying electrochemically active biofilms Examples of technologically relevant electrochemically active biofilms Interpreting results of biofilm studies using the model of stratified biofilms Introduction Conceptual model of stratified biofilms Interpreting results of biofilm studies using the conceptual model of stratified biofilms Using the model of stratified biofilms to refine conceptual models of biofilm structure and activity Computing biokinetics parameters in stratified biofilms Mathematical modeling of biofilm processes and experimental verification of model predictions Protocols and procedures Introduction Preparing the experimental system Quantifying microbial growth Preparing and operating biofilm reactors Common procedures Disclaimer