Tracing modern and fossilized microbial life in natural systems, and exploring genetic and metabolic diversity, energy sources, and biogeochemical transformations at the appropriate scale remains highly challenging. In order to jointly characterize microorganism communities and the mineral environment in which they occur, we have combined approaches of molecular biology (fluorescence in situ hybridization and immunodetection) with an array of high-resolution imaging techniques: coupled CLSM/Raman microscopy and FTIR microspectroscopy, transmission and scanning electron microscopy, synchrotron-based X-ray microimaging and absorption spectroscopy, and in situ stable isotopes analyses by (nano)SIMS.
Several methodologies and protocols of sample preparation adapted to these techniques have been optimized by our group. Altogether they allow localizing specifically remnants of organic matter but also individual prokaryotic cells, and investigating their phylogenetic affiliation at the micrometric scale while characterizing concomitantly the nature and the structure of their microhabitats and past interactions (i.e. mineral dissolution and metabolic byproducts such as biomineralization).
In recent years these techniques were increasingly implemented on natural samples and our ability to reveal chemical, mineralogical, genetic and metabolic diversity at the micrometric scale in subsurface environments was one of the main keys to the high-impact studies (GAP publication list).