Most bacteria and all archaea possess as outermost cell envelope so called surface-layers (S-layers). These layers were formed by self-assembling proteins having a number of habitat depending interesting intrinsic properties. As example, S-layers from bacterial isolates recovered from heavy metal contaminated environments have outstanding metal binding properties and are highly stable. Thus they selectively bind several metals with different affinity. For using S-layer proteins for metal bioremediation and recycling three aspects of the metal-interactions with S-layer proteins must be taken into account. First, S-layers possess different functionalities, e.g. carboxyl, phosphoryl groups, binding toxic metals and metalloids, like U(VI) and As(V), nonspecifically depending on pH. Second, precious metals like Au and Pd are likewise nonspecifically bound to functional groups, but presumably covalently, making the binding irreversible. Third, intrinsic specifically bound metals, e.g. Ca²⁺, are needed for native protein folding, self-assembly, and the formation of highly-ordered lattices. Their binding sites also allow selective binding of chemical-equal elements including the trivalent rare earth elements, possessing comparable ionic radii. Thus this study combines older and recently generated results regarding the metal dependent binding behavior of the S-layer proteins. It enables the development of biohybrid materials for the separation, removal or recovery of strategic relevant metals from natural occurring or industrial waste waters using pH-value as regulating parameter for selective metal binding and also conceivably release.