Prokaryota in natural environments form biofilms, which are benthic assemblages of a variety of microorganisms embedded within their extracellular mucilage. Biofilms are firmly attached to surfaces such as aquatic sediments. Quorum sensing by the many microbes in a biofilm is collective decision making and cooperation for responding to internal and external parameters affecting the community. This communication is based on chemical signaling affecting gene expression of the microorganisms. Microorganisms situated in a biofilm change behaviors and metabolic activities to comply with the requirements of the entire biofilm cooperative. Consequently, reconstruction of the evolution of prokaryotes in Earth history must consider the biofilm way of microbial life. Biogenic sedimentary structures might not represent certain microbial groups, but in fact may be relics of modified cooperative microbial activities. Future research should focus on detectable biosignatures caused by biofilm consortia as a whole instead of on the appearance or extinction of individual microbial groups. Such sedimentary structures as stromatolites and microbially induced sedimentary structures (MISS) are intrinsically controlled by biofilms, but also affected by extrinsic (environmental) conditions.