Geological Digressions

Mineralogy of carbonates; cements

Mineralogy of carbonates; sea floor diagenesis

Mineralogy of carbonates; Beachrock

Mineralogy of carbonates; deep sea diagenesis

Mineralogy of carbonates; meteoric hydrogeology

Mineralogy of carbonates; Karst

Mineralogy of carbonates; Burial diagenesis

Mineralogy of carbonates; Neomorphism

Mineralogy of carbonates; Pressure solution

There is a vast, and for the most part excellent literature on carbonate diagenesis. Here are a few classic and more recent texts that provide much more detail on the subject.

Robin G.C. Bathurst, 1976. Carbonate Sediments and their Diagenesis. Elsevier, Developments in Sedimentology, 12. 658p. An example of the longevity and utility of one of the best on this topic. Now also as an ebook.

Noel James and Phillip Choquette.1984. Diagenesis 5. Limestones; Introduction and subsequent articles on sea floor, meteoric and burial diagenesis. The Canada Geoscience Series on Carbonate Diagenesis is available from the CGS archive.

Noel James and Brian Jones. 2015. The origin of carbonate sedimentary rocks. American Geophysical Union, Wiley works, 464p.An excellent recent update.

Peter Scholle and Dana Ulmer-Scholle, 2003. A colour guide to the petrography of carbonate rocks: grains, textures, porosity, diagenesis. AAPG Memoir 77. Loaded with images.

R.C. Surdam, L.J. Crossey, E.S. Hagen, & H.P. Heasler. 1989. Organic-inorganic interactions and sandstone diagenesis. AAPG, v.73, p. 1-23.

SEPM Strata. Diagenesis and porosity. Part of SEPM’s online stratigraphic web contructed originally by Christopher Kendall. An excellent resource for pretty well anything sedimentological and stratigraphic. Continually updated.

Erik Flugel. 2010. Microfacies of carbonate rocks: Analysis, interpretation and application. Springer. The ebook is cheaper

Mineralogy of carbonates; basic geochemistry

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Some basic geochemistry of carbonates, carbonic acid and carbon dioxide

This is part of the of How To…series… on carbonate rocks

Sedimentary carbonate petrology is concerned first and foremost with the precipitation and dissolution of mineral phases; principally calcite, aragonite and dolomite. Both processes involve chemical reactions and the two primary requirements for these reactions are:

thermodynamics – there needs to be sufficient energy to drive the reactions, and
an excess or deficit of dissolved mass that, for the minerals of interest, includes Ca²⁺_(aq), Mg²⁺_(aq), and CO₃^2-_(aq) (aq = aqueous)

All sedimentary carbonate reactions at the surface or during sediment burial take place in water: fresh water, sea water, or concentrated brines. Furthermore, the chemical composition of these fluids can evolve, for example during burial (sea water to brine), or uplift and exposure (sea water to fresh meteoric water). Such changes are commonly manifested as cement stratigraphy (e.g. high-Mg calcite overlain by low-Mg calcite), or where clasts, matrix and early cements are replaced by new generations of calcite or dolomite.

We are also interested in carbonate reactions because of the present trend towards climate change and the possibility that ocean chemistry may change; ocean acidification tops the list here. To get beyond the hyperbole, to determine whether this is a real possibility or not, we need to understand some basic chemistry. Some introductory concepts are outlined herein.

To delve deeper into the complexities of the carbonate system, have a read of the contributions cited below. Continue reading →

The mineralogy of carbonates; classification

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A post in the How to… series on carbonate mineralogy – limestone classification

The classification of carbonate rocks, like that of sandstones, has gone through a few iterations. Two schemes have stood the test of trial and error, in the field and through microscopes; both were compiled in the late 1950s – early 60s, each serves a slightly different purpose, both are still popular. They are the classification schemes of R. Folk (1959, 1962), and R. Dunham (1962). These two schemes form the backbone of modern carbonate classification and are summarized here, but keep in mind that quite a few iterations have been published.

Folk’s classification scheme

Folk’s scheme for carbonates is in some respects like the one he devised for terrigenous sandstones. It is based on the proportions of matrix, in this case lime mud, and framework components that are mostly allochems (grains that have been subjected to some degree of transport). At one end if the spectrum there is pure mud, or micrite; at the other end clast-supported frameworks with no mud. The spectrum of textures also reflects the energy of the depositional system. The pore volumes in clast-supported limestones are filled with cements, commonly sparry calcite mosaics, some with micritic cements. The degree of grain sorting in these sparites also increases. Grain size follows a relatively simple size-class like the Wentworth scale:

Lutites, 0.004 – 0.062 mm, that are approximately equivalent to mud (silt and clay)
Arenites, 0.062 – 1.00 mm (very fine- to coarse-grained sand)
Rudites, 1.00 mm to boulder range

Folk’s limestones are classified as either micrites or sparites with qualifiers added for the kinds of allochems (ooids, pelloids, fossils and intraclasts) and grain size. Identification of the allochems usually requires a microscope. Hence, Folk’s scheme is best applied to thin sections.

Folk extended this basic classification to include the percentages of micrite and spar cement (diagram below). The cut-off percentage between pure micrite and a micrite with allochems is 1%, 1-10% skeletal fragments is a fossiliferous micrite, 10-50% a sparse biomocrite, and >50% a packed biomicrite. Other qualifiers like pelloids and ooids use the same designations. Thus, an oosparite may be an unsorted oosparite, or if matrix-supported a sparse oomicrite.

Rigid structures like reefs and bioherms were placed in a category of their own – biolithite. The category dismicrite refers to micrite that has been disturbed by burrowing or erosion where voids have been filled by sparry calcite (i.e. disturbed micrite). However, it may be difficult to distinguish between a dismicrite and a micrite that has undergone partial recrystallization to calcite spar.

Dunham’s classification scheme

This scheme is more applicable to outcrop, hand specimen and drill core. It too is based on textural attributes but only those acquired during deposition (which means cements are excluded). His scheme uses three basic components:

The proportion of mud that differentiates between muddy limestones and grainstones (the latter having no mud),
The percentage of grains giving us a mudstone, wackestone or packstone, and
The presence of binding agents (mostly biological) giving us a boundstone.

Both Folk and Dunham apply a separate catch-all category of biolithite and boundstone respectively, for limestones containing fossils and inorganic structures bound by algal mats and more rigid frameworks like corals, stromatoporids and bryozoans. One could apply a qualifier, such as stromatoporoid boundstone, but this gives little paleoenvironmental information on the kinds of structures involved. While working on some Devonian reefs in the Canadian Arctic, Embry and Klovan realized that additional classification categories were required to fully describe the limestone structures they encountered. Their classification became an expansion of Dunham’s scheme, the basics of which have also stood the test of time, albeit with the odd modification.

Embry and Klovan added three new categories:

Bafflestone where organisms trap sediment. By their own admission, Embry and Klovan note that identification of organisms responsible for trapping is equivocal.
Boundstone where material is bound by encrusting and binding organisms, such as calcareous algae and cyanobacterial mats, and
Framestone that is constructed by framework-building organisms like corals and stromatoporids.

So which scheme does one use? The popularity of either scheme depends on which text or journal paper you read – some say Dunham’s scheme, others Folk’s scheme. It is also the case that the two are used interchangeably. If your study focuses on field and outcrop, then Dunham is the logical choice; if the focus is petrographic and thin section then Folk. And if you incorporate outcrop and microscope work, then perhaps use both schemes with cross-referenced rock names. To some extent it depends on personal preference.

Carbonate students should also look at an evaluation of these two popular schemes by Stephen Lokier and Mariam Junaibi. (2016). This paper (open access) looks at some of the modifications to both Folk and Dunham schemes. They find Dunham’s scheme (or modifications thereof) is the most popular. Their own modified scheme is shown below; note that Bafflestone is no longer used here.

*From Sedimentology, v 63, p. 1843-1885, Figure 12 – see link above)

Other post in this series:

Mineralogy of carbonates: Stromatolite reefs

Important literature contributions

R.J. Dunham, 1962. Classification of carbonate rocks according to depositional texture. In W.E. Ham (editor), Classification of carbonate rocks. American Association of Petroleum Geologists Memoir 1, p. 108-121.

A.F. III. Embry and J.E.Klovan, 1971. A Late Devonian reef tract on northeastern Banks Island, N.W.T. Bulletin of Canadian Petroleum geology, v.19, p. 730-781.

R.L. Folk, 1959. Practical petrographic classification of limestones. Bulletin American Association of Petroleum Geologists, v. 43, p. 1-38.

R.L. Folk, 1962. Spectral subdivision of limestone types. In W.E. Ham (editor), Classification of carbonate rocks. American Association of Petroleum Geologists Memoir 1, p. 62-84.

C.St.J.C. Kendall and P. Flood, 2011. Classification of carbonates. In D. Hopley (editor) Encyclopedia of Modern Coral Reefs; Structure, Form and Process. Springer, p. 193-198.

The mineralogy of carbonates; lime mud

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A post in the How to… series on carbonate mineralogy – carbonate mud

Micrite – a sensible contraction of microcrystalline calcite

Lime muds are important components of most shallow carbonate-forming environments: platforms, platform margins and slopes, back-reef and fore-reef settings, and lagoons. They also accumulate in shallow alkaline lakes and as oozes on the deep ocean floor. Like their terrigenous cousins, they accumulate as discrete beds and as matrix to coarse-grained carbonate frameworks.

Lime mud, or micrite includes aragonite and calcite (and perhaps dolomite) having crystal dimensions less than 4-5 microns. Thus, any detailed study requires an SEM or similar technology. Their grain size, and hence high unit-volume surface area means they are quite reactive and prone to recrystallization to coarser calcite-dolomite spar mosaics.

Today, the largest volumes of carbonate mud are produced in shallow warm seas at depths usually less than 10 m. All carbonate mud is produced by precipitation, either directly (i.e without biological intervention), or as a by-product of biological activity. Although there is a degree of certainty about this, the relative contribution of each source remains contentious, even after decades of study. Volumetrically less significant but perhaps no less important sources of mud include bioerosion and mechanical breakdown of skeletal material.

Several species of green algae produce micron-sized aragonite needles and plates that are shed when the alga dies. Of these, the codiacean algae Halimeda and Penicillus are the most prolific producers. For example, in Florida Bay and reef measurements of Penicillus’ aragonite productivity (as needles 2-3µm long) indicate that this species alone can account for all the mud deposited there (Stockman et al. 1967). Other codiacean species plus breakdown of skeletal material also contribute mud, but at this location Penicillus is it. The aragonite produced in these shallow waters is also transported to tidal flats and farther offshore.

Across the ditch, Grand Bahama Bank also hosts swaths of aragonitic mud. Calculations like those penned for Florida, demonstrate that most of this mud (on a volumetric basis) could also have come from codiacean algae. However, this is disputed by Milliman and others who contend that a large proportion of the micron-sized aragonite (up to 75%) precipitated directly from sea water because:

The aragonite crystal morphology is more like that produced by direct precipitation, and
The strontium content of the mud is too high – Sr/Mg ratio ≈ 4 compared to average values of ≈ 2 for codiacean algae.

One phenomenon that has aroused interest as a potential source of aragonite mud is the spontaneous development of milky white clouds of suspended carbonate, or whitings. They form over shallow platforms and persist only as long as it takes for the suspension to disperse or fall out of suspension. Two mechanisms are frequently invoked as explanations:

Where bottom muds are stirred up by feeding fish (this has been observed), and
By direct precipitation from seawater. Measurement of whitings over Grand Bahama Bank show that most of the suspension is micron-sized aragonite, but up to 20% high Mg-calcite may be present (Shinn et al 1989).

Some support for the direct precipitation hypothesis is linked to examples of whitings in areas devoid of bottom-dwelling red and green algae (e.g. Trucial Coast). However, this does not preclude the possibility that suspended algae may play a role. J.W. Morse has suggested that en mass precipitation of aragonite in normal seawater can occur if phytoplankton photosynthesis (during algal blooms) reduces dissolved CO₂.

The Bahamian aragonite is also transported to tidal flats and shallow lagoon, and to the platform margin where it accumulates from suspension on the adjacent deep water slope; carbonate mud that accumulates in this way is called hemipelagic mud.

During the Late Paleozoic, the calcareous algae niche was occupied by phylloid algae that were responsible for building mud mounds. Classic examples are found in Pennsylvanian cyclothems of Kansas and Oklahoma. Here they form part of the regressive limestone facies, where bladed and leaf-like phylloids acted as structural frameworks for the buildups. The facies has been well summarized by Phil Heckel (and lots of references therein).

Precambrian carbonate mudrocks (mostly dolomitized) are invariably associated with stromatolites of all shapes and sizes, from simple laminar mats to complex buildup reef-like structures like the example shown at the top of the post . It is generally understood that their construction was promoted by prokaryotic cyanobacteria (Phanerozoic red and green algae are all eukaryotes). Sedimentological evidence indicates that, like their Phanerozoic counterparts, they too inhabited shallow marine shelf, platform and inter-supratidal environments (here’s a link to the Stromatolite Atlas).

However, carbonate mud was deposited on the outer edges of platforms and adjacent slopes. An example from Belcher Islands (Costello Formation) consists of thin bedded dololutites and calcilututes, with the odd calci-turbidite, but no evidence of cryptalgal laminates. These deposits are also thought to have accumulated from mud suspended in the water column (i.e. hemipelagic) that originated in the carbonate mud ‘factory’ on the shallow platform.

Deep sea oozes are composed primarily of coccoliths and planktonic foraminifera that live in uppermost ocean waters (in the photic zone), and when dead gradually sink to the sea floor. Oozes accumulate in oceanic regions that are devoid of terrigenous sediment.

links to other posts in this series

Mineralogy of carbonates: Stromatolite reefs

The mineralogy of carbonates; non-skeletal grains

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A post in the How to… series on carbonate mineralogy – non-skeletal components

Ooids, pisoids, oncoids and pelloids comprise the most common non-skeletal component of limestones. The first three are characterized by enveloping laminations that range from perfectly concentric spheres to strongly asymmetric grains. They are all products of calcite and aragonite precipitation at the sediment-water interface or within the vadose zone of shallow burial. Although non-skeletal, there is mounting evidence that their formation is influenced, even promoted by biological activity, particularly by bacteria, fungii and algae.

Ooids

Having the opportunity to study modern ooids must be a real treat; a fortuitous circumstance that puts the sedimentologist fair and square in the balmy Bahamas or Trucial Coast (Arabian Gulf). Oh well, I got to spend field seasons in the Canadian Arctic.

Modern sea-going ooids presently form in tropical settings that promote precipitation of aragonite and high-Mg calcite. Ooids are spherical to subspherical grains, characterized by concentrically layered, micron-sized calcite or aragonite crystals. Bahamian ooids are generally 0.5 mm diameter and less. Their cortex consists of micron-sized aragonite crystals that are organized roughly tangential to grain surfaces. The cortex usually envelops a nucleus of skeletal debris, foraminifera or fecal pellets. Variations on this theme are found in some saline lakes where the cortex is a radial array of acicular microcrystals (calcite and aragonite) around a nucleus (e.g. Great Salt Lake, Utah). Ooids are also documented from Precambrian iron formations and Phanerozoic iron-rich deposits where the cortex consists of iron oxides.

Swaths of ooid sediment blanket the Great Bahama Bank beneath clear waters no deeper than 5-10 m. Along the Trucial Coast they accumulate in shallow high energy tidal deltas associated with barrier islands and lagoons. Ooids are subjected to waves and tidal currents, that polish, and sort them according to grain size. Bedforms abound, ranging from large sand-waves (subaqueous dunes) to ripples. Ooids may also be mixed with skeletal debris and pelloids (limestones with ooid frameworks are called oolites). The propensity for ooids to form in shallow, high energy depositional settings makes them excellent paleoenvironmental indicators.

Ancient ooids also display concentrically layered cortices but invariably they are composed of radially fibrous or acicular calcite. In thin section and under polarized light the radial fabric gives rise to an extinction cross centered on the ooid nucleus, that rotates with the microscope stage. This begs the question ‘were the ooids originally calcite (high or low Mg) or aragonite?’. Those that were originally calcite may preserve in fine detail the radial pattern and concentric layering. In contrast, calcite that has replaced aragonite tends to lose some (but not all) of this textural detail. The question is complicated further if the calcite in either case shows any degree of recrystallization – this usually results in larger crystals that destroy original textures and fabrics. Dolomitization tends to exacerbate this problem.

The origin of ooids has been a topic of discussion for at least the last two centuries: explanations ranging from fish eggs to mechanisms invoking snowball accretion of aragonite, from the purely physico-chemical (with no biological interference) to purely biological. Take a look at the excellent summary of past and current ideas in a review by Harris, Diaz and Eberli (2019). What is known is that, whether aragonitic or calcitic, they are the product of direct precipitation from seawater or saline lake water. Research over the last few decades has also shown that biological mediation by microbes is also a critical factor in the formation of ooids.

The association of organic matter, algal filaments, bacteria and fungii enmeshed with aragonite crystals in ooid cortices has been known since the 1950s. These early discoveries promoted the idea that the organic matter and microorganisms changed the chemical microenvironment at sites of crystal growth (pH and the activity of Ca2+ and CO3 2-). While it is likely these biochemical processes do operate, it is now understood that microorganisms play a more complicated role in carbonate biomineralization by creating an organic template that fixes Ca2+ and CO3 2- ions and provides sites for crystal nucleation.

Pisoliths and pisolites

Pisoliths (or pisoids) bear a superficial resemblance to ooids, but are larger (>2 mm) and concentric layering is more irregular. A classic case of misinterpreted pisoliths lies in the Permian Capitan Reef complex (Texas). Originally interpreted as sedimentary and of algal origin (concentric layering of algal laminates), R. Dunham (1969) concluded that they had formed as concretionary structures within the rock column, specifically the vadose zone of subaerially exposed carbonate deposits. The Capitan Reef structures grew by progressive in-situ calcite and aragonite precipitation (the cemented rock is a pisolite). The vadose zone occurs between the land surface and the watertable (sometimes called the unsaturated zone). Sediment within the vadose zone is wetted when the watertable rises, and by surface water infiltration during precipitation events. Thus, carbonate precipitation is a periodic process associated with alternating sediment wetting and drying. Pisoliths may grow competitively producing fitted contacts. Downard elongation of laminae, another characteristic feature, is probably a response to the gravity-driven seepage. There may also be periods of carbonate leaching that remove segments of the pisoliths; subsequent regrowth will result in discordant sets of carbonate layers.

Vadose zone pisoliths are excellent indicators of subaerial exposure and ancient soil-forming conditions, particularly carbonate paleosols or caliches.

Oncoids and oncolites

Oncoids are rounded, spherical to oblate, laminar growths of algae around a nucleus (shells, mud intraclasts, broken lumps of algal crust). Their dimensions are measured in centimetres. The algae usually associated with oncoids are the cyanobacteria (of stromatolite fame). They grow at the sediment surface in supratidal (including sabkhas), intertidal and shallow subtidal environments that are agitated by currents and waves, and perhaps frequented by storm surges. Oncoid laminae grow asymmetrically while the oncoid is at rest, and discordantly when growth has been interrupted by clast jostling and rolling.

Pelloids

The term pelloid refers to any grain that is an aggregate of micro- to cryptocrystalline carbonate. Most pelloids are spheroidal and sand sized; there is little or no internal structure. If they are known to be fecal then they are called pellets. Otherwise, the term pelloid should be used.

Pellets are very common in lower energy settings like lagoons; walk over any tidal flat strewn with gastropods and there will be countless mounds and ribbons of fecal pellets. Fecal pellets contain high proportions of organic matter that break down to organic acids during burial. Their softness also means that grains are susceptible to compaction. Closely packed pellets will tend to merge into a single mass to the point where individual grains become indistinguishable; the end product may be a micrite that is indistinguishable from non-pelloidal deposits.

Like other micrites, pelloidal limestones are susceptible to recrystallization. Note that the term pelloid is also used for skeletal fragments that have been micritised by endolithic algae and fungi.

links to other posts in this series

Bivalve shell morphology for sedimentologists

Gastropod shell morphology for sedimentologists

Cephalopod morphology for sedimentologists

Bivalve shell morphology for sedimentologists

Mineralogy of carbonates – skeletal grains

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A post in the How to… series on carbonate mineralogy

Like sandstone, limestones are made up of framework components, variable amounts of matrix, and cements. Frameworks, or allochems, consist of skeletal fragments, non-skeletal clasts like ooids, pellets, and lime-mud rip-ups (micrite) that have all been subjected to some degree of transport (sometimes very little). Unlike sandstone, the lithification of allochems begins at the sea floor and continues during burial; the products of lithification involve the transformation of calcium carbonate polymorphs, and precipitation of cements (calcite, aragonite, dolomite), sometimes referred to as orthochems. Skeletal and non-skeletal grains plus cement are all used to describe and classify limestones.

The skeletal components of limestone are largely sourced from invertebrates, a wonderfully diverse group of animals that are domicile on the sea floor, within its sediment, and in the water column above. Invertebrate skeletal material may survive intact, or as fragments resulting from mechanical breakdown, bioerosion, or the end product of a vertebrate’s dinner. The preservation potential of all this material is high.

Corals, the foundations of reef complexes, are a dominant component of tropical limestones (reef top, fore-reef, back-reef and lagoon). During the Paleozoic this niche was also occupied by Stromatoporids, and during much of the Precambrian by stromatolites buildups, or reefs. Echinoids, various molluscs (particularly bivalves and gastropods), brachiopods, benthic foraminifera and sponges are common co-inhabitants. Calcareous algae as encrusting forms and the lime-mud producers Halimeda and Penicillus are important contributors to the carbonate factory.

Cool and temperate-water limestones lack coral reefs although solitary corals do occur. Instead, these limestones form from accumulations of bivalves, gastropods, echinoids, forams, and associated attached or encrusting benthic critters like barnacles, bryozoans and calcareous algae; Halimeda, Penicillus and other lime-mud producers do not inhabit cool-temperate seas. Although not reef-like, some species such as oysters commonly construct significant buildups; the Oligocene Te Kuiti Group in New Zealand has some excellent examples.

All these critters, phytoplankton and algae inhabit the photic zone, the uppermost layer in lakes and seas where photosynthesis can take place. The depth to which light penetrates is highly dependent on water turbidity. In clear water 50% of light is absorbed at one metre depth and 90% at 20m. There is little significant light below 200m depth. The photic zone is of critical importance for algae photosynthesis – algae are a primary food source for many invertebrates or join with them in symbiotic relationships.

In tropical-subtropical environs, sea-floor cements include calcite (high- and low-Mg varieties) and aragonite. Sea floor cementation of temperate water carbonates does occur but usually with calcite alone.

Some examples of the important limestone skeletal components are shown below. However, it is important to recognize the limitations when identifying individual fossil grains in hand specimen and with an optical microscope:

The fragments you are viewing will probably be at some random, unknown orientation.
Depending on orientation, the internal structural organization of crystals may be similar across a range of species.
The original skeletal fabrics may be disrupted and even completely obliterated by recrystallization or mineral replacement. Dissolution of skeletal grains also produces moldic porosity.
In general, your identification will probably get no further than class level – if you can distinguish bivalve from gastropod, even bivalve from brachiopod, you are doing well.

Before launching into the unknown, it is worthwhile spending time with thin section – grain mounts of known invertebrates, microfossils and calcareous algae. These will avail you of their attributes and help demonstrate some of the problems noted above.

Microscopic skeletal structures

Skeletal structure in most invertebrates (shells, corallites, tests) consists of microscopic and submicroscopic calcite and aragonite crystal aggregates organized in layers. The orientation and composition of crystallites is highly variable among phyla, classes and even genera. Molluscs commonly have two or three layers of aragonite or alternating calcite-aragonite layers. Nacreous layers that commonly show beautiful coloration on shell inner surfaces (common in bivalves, gastropods and ammonoids), are always aragonitic. Here the aragonite crystals are stacked plates or prismatic clusters, or both. Other layer types in molluscs might include foliated calcite crystals (where the extinction figure sweeps across the skeletal grain), and various combinations of herringbone-like growths of microscopic needle crystals.

Brachiopod shells generally have two layers – modern genera are mostly low Mg calcite. Modern echinoderms tests consist of interlocking plates and spines; each plate and spine is a single high Mg calcite crystal. Echinoid plates and spines are highly porous and under the microscope appear like large ‘poikilitic’ calcite crystals. Calcite cements tend to grow as syntaxial overgrowths on these crystals (i.e. the cements are in optical continuity with the host crystal).

Oblique sections through echinoderm spines in modern Hawaiian beachrock. Note the distinctive radial pattern of single crystal growth and pores between each radial ‘spoke’.

Modern Scleractinian corals are composed of aragonite fibers or needles organized into radiating clusters, or spherulites. Extinct groups such as Rugose and Tabulate corals consist of low Mg calcite fibers, but these may have recrystallized from high Mg calcite or aragonite. In thin section, the fibrous clusters plus the overall coral structure that includes the radiating septa (solid walls separating the cavities) are useful identifiers.

Modern bryozoans consist of high Mg calcite, aragonite, or both as microscopic and submicroscopic crystals. In thin section fragments of bryozoans are best recognized by their fenestrate structure – a regular arrangement of chambers, usually in pairs, that housed each animal (bryozoans are colonial structures).

Foraminifera are mostly calcitic, although some groups like Globigerina and related families are aragonitic. Like the other phyla, foraminifera wall structures are variable – common types are fibrous (normal to the test wall), granular, and microgranular or micrite-like.

Calcareous algae are another equally diverse group that are important limestone contributors. Common encrusting forms like Coralline algae are mostly high Mg calcite where individual crystals are submicroscopic that collectively form intricate arcuate or wavy layers. One common species, Lithothamnion, commonly encrusts pebbles and cobbles and typically is found along high energy rocky coasts.

Calcareous green algae such as Halimeda and Penicillus produce aragonite needles. Across the shallow sea floor (within the photic zone) carpets of green algae produce large volumes of aragonitic lime mud, or micrite – more on this in the companion Lime mud post.

Planktonic algae such as Coccoliths are composed of low Mg calcite. They too are important contributors to lime mud – but you will need a scanning electron microscope to see them.

links to other posts in this series

Gastropod shell morphology for sedimentologists

Cephalopod morphology for sedimentologists

Mineralogy of Carbonates

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This is the first of a How To…series… on carbonate rocks – the mineralogy of calcite, aragonite and dolomite.

If the arithmetic is correct, limestones and dolostones make up about 5-10% of sedimentary rocks in Earth’s crust. They host freshwater aquifers, mineral deposits, hydrocarbons, and some pretty spectacular landscapes (like caves and karst landforms). We treat carbonate rocks separately from sandstones for several reasons:

Their framework components are primarily of biological origin, either directly as skeletal material or indirectly where organisms like algae and bacteria mediate carbonate mineral precipitation,
All these critters inhabit the photic zone, The depth to which light penetrates is highly dependent on water turbidity. In clear water 50% of light is absorbed at one metre depth and 90% at 20m. There is little significant light below 200m depth. The photic zone is of critical importance for algae photosynthesis – algae are a primary food source for many invertebrates or join with them in symbiotic relationships.
Carbonate chemistry is fundamentally different to the siliciclastics, and dominated by three minerals – calcite, aragonite, and dolomite,
They tend to be chemically reactive at Earth’s surface and during all stages of burial,
Limestones form at all latitudes, but the biomass responsible for their accumulations is most prolific in tropical and subtropical environs.
Cementation of limestones begins at the sea floor and continues during burial. Original components like aragonite and high-magnesian calcite are usually replaced by calcite or dolomite during burial. In contrast, cementation of arenites does not begin until after burial.
Oceanic limestones (like foraminiferal ooze) tend not to accumulate at depths greater than about 4000-5000m – the calcite-aragonite compensation depth.

Carbonate mineralogy: optical properties

Calcite:

CaCO₃
Hexagonal crystal system.
Crystals shapes are varied: commonly as rhomohedra and scalenohedra but can occur as clustered prismatic needles.
Under Polarized light it has high birefringence and appears to twinkle as the microscope stage is rotated. Relief changes from high to low during stage rotation.
Excellent rhombohedral cleavage.
Twin lamellae are common and generally parallel or oblique to the long rhombohedral diagonal.
Uniaxial negative.
Sedimentary calcite can incorporate up to 19 mole% magnesium in its crystal lattice. High magnesian calcite has >5 mol% Mg; low magnesian calcite <5%. The magnesium content of skeletal calcite seems to fall into two groups; <5 mole %, and 11-19 mole %. Ferroan calcite has up to 2-3 mole% Fe²⁺. Common methods used to distinguish these various forms are noted below.

Aragonite:

CaCO₃. Can have up to 10,000 ppm strontium (high Sr is common in many recent corals, ooids and calcareous algae.
Aragonite is a polymorph of calcite but belongs to the orthorhombic crystal system.
Mostly commonly as acicular and fibrous cements in limestones, and a common component of invertebrate and protist skeletal material.
High birefringence.
Biaxial negative.

Dolomite:

CaMg(CO₃)₂. The crystal lattice contains alternating layers of CaCO₃ and MgCO₃. Highly ordered dolomite contains equal amounts of Ca and Mg. Protodolomites, found in modern hypersaline lagoons and sabkhas, and recently discovered in some calcareous algae, have disordered crystal lattices (on XRD diffractograms) and less Mg.
Hexagonal crystal system, usually as rhomobedra. Commonly seen as a replacement of calcite and aragonite, in some cases the original textures are preserved, and in others they are completely obliterated.
Twinning less common. Twins parallel the short and long rhombohedral diagonals.
Very high birefringence and usually very high relief.
Uniaxial negative

Some popular methods for detecting and distinguishing dolomite and the polymorphs of calcite include:

Staining

Chemical staining of thin sections and rock slabs may seem a bit unsophisticated in an age where the technology for detailed analysis of mineral assemblages is readily available. But for the common carbonate minerals the method can be a very useful first pass at identification. The two stains in common use, Alizarin red-s (ARS) and Potassium ferricyanide (PF), are cheap and easy to use, even in the field where they may give an indication of stratigraphic trends in mineralogy, for example calcite/dolomite ratio, or changes in ferroan calcite. ARS is used to distinguish between calcite (stains pink-red) and dolomite (no stain). The intensity of blue PF stains in ferroan calcite increases with increasing Fe content; ferroan dolomite stains in green hues.

XRD

Diffraction peaks in an X-ray diffractogram measure the spacings between planes of atoms in a crystal lattice; they are referred to as d-spacings. A characteristic peak in Ca-Mg carbonates is the ‘104 peak’ that increases or decreases according to crystal chemistry. XRD measurement of the 104 peak is one of the more useful methods for identifying the magnesium content of calcites and identifying basic mineralogy in fine-grained deposits.

Cathodoluminescence

Pure calcite and dolomite do not luminesce when exposed to a high energy electron beam. However, certain impurities in the crystal lattice may become excited enough to luminesce, emitting light at visible wave lengths. The most common luminescence activator in carbonates is manganese (Mn²⁺), which emits orange-red to orange-yellow light. Manganese replaces calcium in the calcite lattice during precipitation. As little as 10-20 ppm Mn will activate luminescence. Note that iron (as Fe²⁺) will quench Mn luminescence if it is present in concentrations greater than a few 10s ppm. Iron as Fe³+, cobalt (Co²⁺) and nickel (Ni²⁺) will also quench Mn luminescence.

The amount of Mn²⁺ incorporated into the lattice will vary during diagenesis in concert with changes in the Mn²⁺ concentration of the interstitial fluids. This is commonly manifested as zoning in crystals, where the emission colours vary from one zone to another. Analysis of luminescence patterns in carbonate crystals can provide valuable clues about diagenetic history, particularly the evolution of cements, evolving fluid composition, and changes to rock porosity and permeability.

Changes in limestone composition through time

We tend to think of limestones as a Phanerozoic phenomenon – those fabulous Devonian, Carboniferous and Permian reefs and platforms. In fact, sedimentary carbonates accumulated across the last 3.5, perhaps even 4 billion years of Earth history. The Precambrian geological record is littered with extensive platform carbonates associated with stromatolite buildups. Most have been dolomitized but there is textural and geochemical evidence of them having been originally calcitic and aragonitic.

Production of skeletal and non-skeletal limestone during the Phanerozoic has not been steady and continuous but has fluctuated on a scale that reflects major changes in plate tectonics. Such grand scale cyclicity was recognised by Fred Mackenzie and John Morse (1992) who noted a tenuous coincidence between high sea levels and high rates of addition of new crust at mid-ocean spreading ridges, and low sea levels with low accretion rates. A burgeoning database now allows us to be more confident about this grand-scale cyclicity. We now know that the coupling of plate tectonics and sea level also produced changes in sea water composition, specifically the Mg/Ca ratio. High rates of accretion result in a lowering of the Mg/Ca ratio because Mg is removed from seawater and Ca is added during hydrothermal alteration of hot new crust. Geochemical experiments and theoretical analyses also tell us that seawater at low Mg/Ca ratios favours precipitation of calcite cements with low Mg content; many molluscs and modern corals also enjoy these conditions. The opposite, high Mg/Ca ratios, are more likely during low sea floor accretion rates (and low sea levels) and promote precipitation of high magnesian calcite and aragonite cements. High Mg/Ca ratios also favour critters like brachiopods, some extinct corals, modern echinoderms and calcareous algae. Thus, 1^st-order low sea level cycles coupled with high Mg/Ca ratios tend to favour aragonite seas and high sea levels with low Mg/Ca ratios calcite seas.

The posts that follow in this carbonate series will deal with: the skeletal and non-skeletal frameworks of limestones, lime mud or micrite, limestone classification, reefs and platforms, cool water limestones, cementation, recrystallization and neomorphism, porosity and permeability – this will do for a start.

links to other posts in this series