This study performed in situ incubation experiment with pyrite (FeS2), Zerovalent iron and basalt glass at the deep seafloor around hydrothermal vent in Izu-Bonin arc. And we simultaneously characterized microbial phylogenetic, mineralogical, and biogeochemical properties in the incubated materials. The microbial community was identified using 16S rRNA gene amplicon seuquence analyses. For the mineralogical and biogeochemical characterizations, synchrotron-based X-ray spectroscopic techniques were applied, which allows us to quantitatively specify secondary minerals and microbial biomolecules formed in the sample with high elemental selectivity and high spatial resolution. In this study, we were able to accurately obtain the microbiological, mineralogical, and geochemical information in the incubated minerals and metals.