In this study, the mineral-weathering bacterium F77, isolated from the soil of a debris flow area, was evaluated for its weathering activity under direct contact with biotite or without contact. Then, biotite-weathering behaviors of strain F77, its mutants that were created by deleting the and genes, which are involved in gluconic acid metabolism and pilus formation, respectively and the double mutant F77ΔΔ, were compared. The relative gene expression levels of F77 and its mutants F77Δ and F77Δ were also analyzed in the presence of biotite. Direct contact with biotite increased Fe and Al release from the mineral in the presence of F77. All strains had a similar ability to release Fe and Al from the mineral except for F77Δ and F77Δ Mobilized Fe and Al concentrations were decreased by up to 72, 26, and 87% in the presence of F77Δ, F77Δ, and F77ΔΔ, respectively, compared to those observed in the presence of F77 during the mineral-weathering process. Gluconic acid production was decreased for F77Δ and F77ΔΔ, while decreased cell attachment on the mineral surface was observed for F77Δ compared to that observed for F77. The F77 genes involved in pilus formation and gluconic acid metabolism showed increased expression levels in the presence of biotite. The results of this study showed the important role of the genes involved in gluconic acid metabolism and pilus formation in mineral weathering by F77 and demonstrated the distinctive effect of these genes on mineral weathering by F77. Bacteria play an important role in mineral weathering and soil formation; although the molecular mechanisms underlying the interactions between bacteria and silicate minerals are poorly understood. In this study, the interactions between biotite and the highly effective mineral-weathering bacterium F77 were characterized. Our results showed that the genes involved in gluconic acid metabolism and pilus formation play important roles in mineral weathering by F77. The presence of biotite could promote the expression of these genes in F77, and a distinctive effect of these genes on mineral weathering by F77 was observed in this study. Our results provide new knowledge and promote better understanding regarding the interaction between silicate minerals and mineral-weathering bacteria and of the molecular mechanisms involved in these processes.