The goal of this project is to develop a new analytical platform for the rapid, high-precision determination of elemental and stable isotopic composition of microbial populations at sufficiently high spatial resolution to localize and quantitatively map bio-essential elements within cells. The analytical approach makes use of a technique, secondary ion mass spectrometry (SIMS), where the sample is bombarded with a focused ion beam, generating secondary ions from the sample itself, which are electromagnetically focused onto a series of collectors. With enhanced ion source and detector capabilities, this instrument will be used to probe the uptake, assimilation, and sub-cellular localization of key elements, isotopes, and biomolecules in a suite of different model microbial systems (cyanobacteria, purple photosynthetic bacteria, and Methylobacterium), which are all promising systems for sustainable bioenergy production. The resulting data will be enable us to link together molecular-scale chemical and isotopic information with biological function to generate whole-cell, systems-level understanding that is currently not achievable using standard SIMS instruments.