Our main goal in this proposal is the elucidation of fundamental interaction processes between microbial systems and a living organism. This research will directly lead us to a so far missing understanding of the detailed mechanism of bacterial pathogen infection in vivo. The newly gained knowledge will be highly important for the development of antibacterial drugs against pathogen-related diseases and for the ultra-sensitive detection of pathogens using bio-sensors.Bacteria have existed for several billion years by adapting to changes in their environment. Understanding how bacteria acquire new functions in response to environmental changes will advance our fundamental knowledge thereby enhancing our ability to design and tailor changes in biological structure. We will investigate local physical and biochemical variation in the bacterial outer membrane of live bacteria, at nanometer resolution, as bacteria interact with both abiotic and biotic surfaces. For these studies we will use Escherichia coli (E. coli) primarily because it has been well studied and the genome sequence has been determined.Biological scanning probe microscopy (SPM) is the tool of choice for these studies because it is the only instrument that allows studying living microbial organisms in their natural environment at the nano-meter scale resolution. A broad range of scanning microscopic techniques including Force spectroscopy, Topography and recognition imaging (TREC), Kelvin probe force microscopy (KPFM), and Scanning microwave microscopy (SMM) will be utilized in these studies for looking into the dynamics of individual protein domains, local binding sites, and locations of charge centers of complex proteins at sub-nanometer, pico-Newton, and nano-Ampere resolution.