Detection and phylogenetic identification of labeled prokaryotic cells on mineral surfaces using Scanning X-ray Microscopy

The involvement of intraterrestrial microbes in geochemical cycles is now well recognized. However, owing to the small number of appropriate methods for probing these ecosystems, the exploration of their metabolic diversity, energy sources, and biogeochemical transformations remains limited. Here we demonstrate the ability of scanning X-ray microscopy using synchrotron radiation to localize and characterize the phylogenetic affiliation of individual prokaryotic cells on various mineral surfaces (e.g. carbonates, basaltic glass) when combined with a newly developed protocol based on fluorescence in situ hybridization coupled to ultra-small immunogold. The possibility to associate simultaneously the phylogenetic identification of microorganisms with the chemical and structural characteristics of associated mineral phases (i.e. inorganic substrate and biomineralizations), offers great interest for assessing the geochemical impact of subsurface microbial communities and unraveling microbe-mineral interactions in the deep biosphere.