A major question in the study of rock varnish involves the process by which Mn-oxide transforms into Mn-minerals that are intimately associated with monolayers of clay. There is increasing evidence that Mn- and Fe-oxide deposition in varnish is microbially mediated, although much of the evidence is circumstantial. Workers have cultured and identified several strains of Mn-oxidizing bacteria from rock varnish, but direct evidence of microbial transformation of Mn-oxide is obliterated by surface weathering in an extremely slow growing environment.

Ferromanganese coatings on cave walls and ceilings represent an environment in which weathering is not a factor, allowing researchers an analogous environment with intact coatings. These deposits, present in several caves in New Mexico and South Dakota, contain variable amounts of clay and Al-oxide minerals, and all are rich in Mn- and Fe-oxides (enriched hundreds to thousands of times relative to the underlying bedrock). Diverse microbial communities have been identified in these cave deposits by 16S rDNA sequence analysis. Closest relatives of some clones are manganese- and iron-oxidizing or nitrogen-fixing bacteria. Exoenzyme rock surface studies in the caves show microbial activity on certain substrates (e.g. acetate). Similar surface rock studies in New Mexico and desert varnish in Utah reveal high levels of microbial activity on many different substrates, indicating the ability of resident microbes to utilize varied carbon sources. The mineralogy and microbiology of the cave deposits bear striking resemblance to rock varnish although the three-dimensional structure is very different.

Like rock varnish, todorokite and birnessite have been identified in the cave deposits along with illite and other clays. Nanocrystalline Fe- and Mn-oxides were confirmed by TEM examination. The oxides show a progression of increasing crystallinity from filamentous forms to fibrous, needle-like crystals to platy crystals. We believe that this progression of Mn-oxidation and crystallization may elucidate similar processes in rock varnish where Mn-coated microbial debris is recrystallized to form the microlaminations that are common in varnish.