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Pyrite (FeS2) is the most abundant iron sulfide mineral found in carbonate sediments. Pyrite is an isometric mineral that commonly forms crystals that are cubic, pyritohedral or octahedral, but it may also form anhedral replacement masses. In sediments, pyrite also occurs as framboids or spheres composed of aggregates of minute crystals. Pyrite is opaque in thin section and is readily identified by reflected light microscopy due to its brassy to golden yellow color (simply holding a strong light source above the thin section as it sits on the microscope stage and blocking transmitted light illumination will generally suffice for identification).

Hematite (Fe2O3) is normally an opaque mineral. In reflected light, hematite is deep red to rusty red. It rarely forms crystals and occurs typically as amorphous masses. Hematite commonly forms through weathering and oxidation of pyrite or other iron sulfides, and it is not unusual to find pyrite and hematite together.

Goethite (FeO(OH)) is an opaque orthorhombic mineral, whereas limonite (FeO(OH)•nH2O) is a cryptocrystalline or amorphous, hydrated form of this compound. Both minerals are reddish brown to yellowish brown in reflected light, and they can be difficult to tell apart from hematite. They are weathering products of either iron sulfides or hematite.

Sphalerite (ZnS) is an isometric mineral that is isotropic in cross-polarized illumination, has a high positive relief, and ranges from colorless to pale yellow or light brown. A slight birefringence may be present when the crystals have been strained. Crystals are usually not well formed, but where present, crystal faces may be curved. Well-developed lamellar twinning is common in sphalerite. Sphalerite is found in Mississippi Valley-type mineralized carbonate rocks and other hydrothermal deposits.

Fluorite (CaF2) is an isometric mineral that forms cubic crystals, although anhedral masses are common in carbonate rocks. Fluorite normally is colorless in thin section, but strongly colored samples may be pale purple to green. Halite and fluorite are easily confused since they are both isotropic, form euhedral cubic crystals and have negative relief. Fluorite can be distinguished from halite based on its well-developed octahedral cleavage, lower negative relief, and color spots that are produced by inclusions within the crystals. Most fluorite was precipitated from hydrothermal fluids and may be associated with Mississippi Valley-type mineralization.

The two most common phosphatic minerals in carbonate rocks are fluorapatite (Ca5(PO4)3F) and hydroxylapatite (Ca5(PO4,CO3,OH)3(F,OH)x). When intergrown, the minerals formed are francolite (crystalline form) and collophane (cryptocrystalline form). Collophane is the more common mineral — it is isotropic to very weakly birefringent with colors that range from yellowish to brownish. Most early diagenetic phosphate is made of collophane. Francolite has a higher relief and low birefringence (gray to low white); it is colorless to pale brown, and may be slightly pleochroic. Diagenetic phosphatic minerals can form amorphous nodular masses, cements or replacements. Diagenetic phosphates form mainly in areas with substantial primary sedimentary phosphate accumulation — areas with low sediment accumulation rates and high nutrient inputs.

Glauconite (K,Ca,Na)1-0.56(Fe3+, Mg, Fe2+,Al)2(Si, Al)4O10(OH)2) is a clay mineral found only in marine deposits. It forms pellets or granules in areas of slow sedimentation. It also precipitates as an early diagenetic mineral replacing clasts or filling porosity in shallow to deep marine settings that have high nutrient levels and low sediment accumulation rates. Glauconite is green to olive green in color and has a greenish birefringence; it can look similar to chlorite, but chlorite is usually more platy and has anomalously low birefringence.

Hydrocarbons can be found as interstitial material in carbonate rocks or as fluid inclusions within carbonate cements. In some cases, hydrocarbons effectively terminate cementation by blocking the entry of aqueous fluids responsible for diagenesis. Bitumen, asphalt and hydrocarbon-filled inclusions all are products of this complex interplay of hydrocarbon-bearing and aqueous fluids. Evidence of hydrocarbon entry includes residues and inclusions, as well as curved meniscus cements and the preservation of unstable carbonate phases, such as aragonite, in very old rocks.

An SEM image of a pyrite framboid. Framboids are almost perfectly spherical bodies of small, interlocking pyrite crystals. These spherical aggregates typically form discrete bodies, but they are also found as clusters or multiple spheroids. They are authigenic in origin and form in reducing environments or in reducing microenvironments associated with decomposing organic matter.

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