Synchrotron based soft X-ray scanning transmission microscopy (STXM) is a powerful tool for spatially resolved chemical analysis. It provides speciation and quantitative chemical mapping of biochemistry and non-biological components (metallic species, minerals, etc) at high spatial resolution (~30 nm) on samples that can be fully hydrated, and thus close to their natural state [1]. The principles and capabilities of STXM will be described and illustrated with literature results in soil science (Myneni et al; Brown et al), and recent studies from my work. The latter includes: • correlative mapping of biofilms by combined STXM, confocal laser scanning microscopy (CLSM), and transmission electron microscopy (TEM) [2] • speciation and quantitative mapping of Ni, Mn and Fe in natural riverine biofilms [3] • Studies of cation exchange on clays [4] • Investigation of mechanisms of organic antimicrobials in pure bacterial cultures (P. Fluorescens) and in mixed microbial (diatom, bacteria) river biofilms. [5]

While these studies have a variety of specific goals, in total, they well illustrate the power and potential of STXM to contribute to improving mankind's understanding of microbial – soil interactions. Research funded by AFMnet Centre of Excellence, NSERC (Canada), CFI, the Canada Research Chair program, and NWRI (Canada). Tolek Tyliszczak and David Kilcoyne are thanked for their expert work on the development and maintenance of STXM. The Advanced Light Source is supported by Office of Basic Energy Sciences of the U.S. Department of Energy. 1. Hitchcock A.P. et al. (2005) J. Electron Spectroscopy 144: 259-269 2. Lawrence J.R. et al. (2003) Applied Environmental Microbiology, 69: 5543-5554. 3. Dynes J.J. et al, (2005) Environmental Science & Technology. in press 4. Gates, W.P. et al, (2006) Clays and Clay Minerals in preparation 5. Dynes J.J. et al, (2005) Nature in preparation