Important evidence for microbial mediation in rock–water interactions has been recognized since the mid-1980s. Bacterial activity has been shown to contribute not only to the weathering and leaching of rocks but also to the deposition of new minerals. One example is the concentration of large amounts of iron and silica in sediments, such as the Banded Iron Formations, which had been difficult to explain by abiogenic physicochemical means alone.

Since the discovery in 1954 of coccoid and filamentous microfossils in the Early Proterozoic Gunflint chert formation of Canada and the United States, it has been realized that microorganisms would likely have influenced the formation of such deposits. Today many of the reactions involved in the deposition of sediments under natural conditions are thought to be microbially mediated.