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A nodule in petrology or mineralogy is a secondary structure, generally spherical or irregularly rounded in shape. Nodules are typically solid replacement bodies of chert or iron oxides formed during diagenesis of a sedimentary rock. Nodules may be hollow as geodes or vugs or filled with crystals and intricate geometric shrinkage patterns as in septarian nodules.
There is an important distinction to draw between nodules and concretions; the latter being formed from mineral precipitation around some kind of nucleus while the former is a replacement body.
Chert and flint nodules are commonly found in horizontal layer in limestone and chalk formations respectively. They form from the recrystallisation of amorphous silica arising from different marine organisms after their death: siliceous spicules of sponges, or debris from radiolaria. Diatoms are also a widespread source of biogenic silica in marine sediments.
Silicic volcanic rocks also form nodular segregations during cooling and recrystallization of rhyolitic and obsidian flows. Thundereggs are geode like nodules that form in volcanic ash deposits during diagenesis.
See also 
- Concretions, formed from mineral precipitation in the pores of a sediment, not to be confused with nodules
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