Which preposition to use with nodule

of Occurrences 10%

But instead of being hard, as Silurian rocks are wont to be, they are mere loose beds of dark sand and shale, yellow with sulphur, or black with carbonaceous matter, amid which strange flakes and nodules of white quartz lie loose, ready to drop out at the blow of every wave.

in Occurrences 2%

Quartz crystals, with chalcedony, from nodules in amygdaloid.

Which preposition to use with  nodule