More black stuff in caves! Hill & Forti cover the topic of manganese oxides and organisms pretty well, however here are some notes on occurrences of manganese deposits in NSW caves.

At Jenolan Caves, there appear to be several types of manganese deposits.

Coatings on pebbles in underground streams:

Here the pebbles are made of a porous, usually non-limestone material such as shales and porphyry brought into the underground system by stream action. The key seems to be porosity and solubility as the manganese-depositing organisms most likely cannot develop colonies on surfaces that get dissolved away. The source of the manganese itself is most likely the breakdown of components of the shale and porphyry rocks upstream entering the water.

Coatings on dolomitized limestone:

Again the material is porous and the key seems to be porosity and solubility. I thought (2001) that source of the manganese was the shale and porphyry rocks hydrologically above the cave.
Later investigations Rowling (2004b), including thin sections of Jenolan Caves Limestone, suggest that manganese minerals are normally present in ferroan dolomite veins (Fe and Mn frequently occur together), and that pyritic weathering allows the manganese to migrate and remain on the surface. One in-cave sample was so weathered it resembled a gooey ball of clay, however thin section revealed a delicate structure formed by the almost complete replacement of micrite by ferroan dolomite, with unaltered larger bioclasts. The ferroan dolomite had been altered (possibly by pyritic oxidation) to a spongy mass of limonite and a dark mineral resembling pyrolusite. The only evidence for pyrite in the sample was tiny dark blood-red cube shapes throughout the structure.

Dark coatings on igneous intrusions exposed in a cave:

Manganese is a common constituent of many minerals which form igneous rocks. Often an igneous intrusion in the bedrock shows up in the cave as a dark rock. As part of the weathering process, unstable minerals such as olivines will gradually form iron oxyhydroxides and manganese-rich minerals in the cave environment.

Dark deposits associated with breakdown rocks:

In the Jubilee show cave, there are areas of bedrock breakdown with interesting deposits of brown and black manganese minerals associated with white minerals. These has not been examined thoroughly yet, and may be associated with bat guano.

Dark deposits associated with red-brown clays:

In the Jubilee show cave, there is a red-brown clay deposit in a vertical crack between two limestone bedrock boulders. On this clay deposit are several white patches with a black/blue annular border. The white patches have small yellow and white spheres. The whole effect resembles a bacterial colony and is about 10 to 20 mm wide. I first noticed it in about 1989 and it hasn't grown much (if at all).

Black, white and yellow laminated flowstone:

In another part of the Jubilee show cave (just before arrival at Cooks Cavern), there is an interesting deposit of flowstone which has been cut through by the track. It appears to be laminated black, white and yellow. In the absence of better information, I am assuming at this stage that the black is one of the manganese oxides, the white is calcite and the yellow is a phosphate (presumably from bat guano).

Black and clear laminated flowstone:

Also at Jenolan Caves there is another interesting flowstone deposit in a cave more widely known for its cloying mud than its decorations (not a show cave). A chamber in Dwyers Cave contains shards of flowstone which is alternately layered clear or flecked with black. The black and clear calcite layers are associated with layers of fine brown mud. This mud seems to be a swelling type of clay. The calcite layers are curved up along cracks, forming a tepee structure, presumably the prototype of a cave shield.

Black and red porous deposits with aragonite

I mentioned this type of deposit before (see Iron). The black layers appear to be manganese oxides, migrating from an altered ferroan dolomite deposit.

There are also soot deposits at Jenolan Caves, usually attributed to smoke from past bush fires. An example of this was seen near the entrance of Imperial Cave, Jenolan Caves, while surveying in an area later used as a power cable duct.