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Bentonite is one of the materials used to construct engineered barriers in high-level radioactive nuclear waste geological disposal with its many advantageous features such as low hydraulic conductivity, self-sealing ability, durability, adsorption and immobilization of metals and radionuclides and reduction of microbial activity. Many of these properties are linked with the bentonite swelling capability. Transformations of indigenous microorganism communities from Wyoming-type bentonite and the Finnish repository site groundwater and their effects on the bentonite structural iron over five years were studied in repository relevant anoxic and oxic slurry conditions. Active sulfate reduction (0.06 nmol mL−1 day−1) was detected in the anoxic microcosm waters after a year, however after two years sulfate reduction was not active anymore. Microbial numbers determined by quantitative PCR in the bentonite slurry of both experiment types supported the finding of decrease of overall microbial activity after a year of incubation that was not maintained anymore by the dissolving organic carbon from the bentonite. Regular electron donor additions (final concentration of 2 mM for formate and acetate each, three times per year) activated the microbiome resulting in increasing numbers of bacterial 16S rRNA gene copies and sulfate reducers (dsr B gene copies) as well as detection of sulfide in the water phase of both experiment types. After 4.9 years the structural iron in the fine portion of the montmorillonite had become completely reduced in all microbial microcosms and minor smectite illitization was detected especially in anoxic microcosms. Dominating bacterial groups at the end of the experiment were mainly known sulfur/sulfate and iron reducers. Archaea and fungi constituted a minor part of the microbiomes. In originally oxic microcosms, the bacterial 16S RNA and dsr B gene copy numbers were lower than in the anoxic experiment but started to significantly increase after the electron donor additions. Microorganisms originating from the repository environment could reduce the bentonite structural iron in a few years to an extent likely to affect the bentonite swelling ability if sufficient amounts of suitable electron donors are available in localized areas where bentonite is not at high density and pressure in the geological disposal. • Inherent microorganisms totally reduced the structural iron in bentonite slurry. • Bentonite DOC maintained the microbial activity for less than two years. • Inherent sulfate and iron reducers benefited from the electron donor additions. • Microbial communities from different sources caused iron reduction in bentonite. • 180 °C for 16 h killed most, but not all bacterial spores in bentonite. [ABSTRACT FROM AUTHOR]