Microorganisms have a tremendous influence on their environment through the transfer of energy, charge, and materials across a complex biotic mineral-solution interface. The bio-modification of mineral surfaces involves the complex action of microorganism on the mineral surface. The manner, in which bacteria affect the surface reactivity and the mechanism of bacteria adsorption, is still unknown and accumulation of the primary data in this area is only starting. The bio-flotation and bio-flocculation processes concern the mineral response to the bacterium presence, which is essentially interplay between microorganism and the physicochemical properties of the mineral surface, such as the atomic and electronic structure, the net charge/potential, acid-base properties, and wettability of the surface. There is an urgent need for developing basic knowledge that would underpin biotechnological innovations in the natural resource (re)processing technologies that deliver competitive solutions.