Geomicrobiological properties of Tertiary sedimentary rocks from the deep terrestrial subsurface

•Microbial colonization experiments in a borehole drilled by a new aseptic skill.•Dominant colonization of Fe(III) reducers matched with groundwater chemistry.•Mechanical, geochemical and microbial results were consistently integrated.•Microbes influenced groundwater redox chemistry and radionuclide transport.

Microbial metabolic activity within the deep subsurface can potentially impact radionuclide migration during geological disposal of nuclear waste. To evaluate the geomicrobiological properties of Tertiary sedimentary rocks, which are widely distributed in the repository environment in Japan, aseptic and deoxygenated drilling was conducted with the installation of a multi-packer system to collect cores and groundwater. Integrated results from measurements on potential rates of denitrification and pore-size distributions in drill core samples indicated that in situ microbial activity is constrained by the availability of pore spaces larger than 0.1 μm in radius. Comparison of geochemical profiles of porewater extracted from the core samples and groundwater collected within multi-packer intervals revealed that terminal electron acceptors such as nitrite and sulfate were depleted in groundwater. Microbial community structures based on 16S rRNA gene sequences were represented by phylotypes related to Fe-, Mn-, elemental sulfur- and sulfate-reducing bacteria in groundwater. In addition, a phylotype closely related to denitrifying Acidovorax sp. of the β-proteobacteria was dominant in the lower borehole interval. From our results, it is likely that groundwater microorganisms mediate redox reactions that influence the mobility of radionuclides in the deep subsurface.