Carbonate Petrography

Carbonate petrography is the study of limestones, dolomites and associated deposits under optical or electron microscopes greatly enhances field studies or core observations and can provide a frame of reference for geochemical studies.

25 strangest Geologic Formations on Earth

The strangest formations on Earth.

What causes Earthquake?

Of these various reasons, faulting related to plate movements is by far the most significant. In other words, most earthquakes are due to slip on faults.

The Geologic Column

As stated earlier, no one locality on Earth provides a complete record of our planet’s history, because stratigraphic columns can contain unconformities. But by correlating rocks from locality to locality at millions of places around the world, geologists have pieced together a composite stratigraphic column, called the geologic column, that represents the entirety of Earth history.

Folds and Foliations

Geometry of Folds Imagine a carpet lying flat on the floor. Push on one end of the carpet, and it will wrinkle or contort into a series of wavelike curves. Stresses developed during mountain building can similarly warp or bend bedding and foliation (or other planar features) in rock. The result a curve in the shape of a rock layer is called a fold.

Showing posts with label diagenesis. Show all posts
Showing posts with label diagenesis. Show all posts

10 of the Best Learning Geology Photos of 2016

A picture is worth a thousand words, but not all pictures are created equal. The pictures we usually feature on Learning Geology are field pictures showing Geological structures and features and many of them are high quality gem and mineral pictures. The purpose is to encourage students and professionals' activities by promoting "learning and scope" of Geology through our blogs.
In the end of 2016, we are sharing with you the 10 best photos of 2016 which we have posted on our page.

P.S: we always try our best to credit each and every photographer or website, but sometimes it’s impossible to track some of them. Please leave a comment if you know about the missing ones.

1. Folds from Basque France

 Image Credits: Yaqub ShahYaqub Shah

2. Horst and Graben Structure in Zanjan, Iran

Image Credits:

3. A unique Normal Fault

4. The Rock Cycle
 rock cycle illustrates the formation, alteration, destruction, and reformation of earth materials, and typically over long periods of geologic time. The rock cycle portrays the collective system of processes, and the resulting products that form, at or below the earth surface.The illustration below illustrates the rock cycle with the common names of rocks, minerals, and sediments associated with each group of earth materials: sediments, sedimentary rocks, metamorphic rocks, and igneous rocks.

Image Credits: Phil Stoffer

5. An amazing Botryoidal specimen for Goethite lovers! 

Image Credits: Moha Mezane 

6. Basalt outcrop of the Semail Ophiolite, Wadi Jizzi, Oman

Image Credits: Christopher Spencer
Christopher Spencer is founder of an amazing science outreach program named as Traveling Geologist. Visit his website to learn from him

7. Val Gardena Dolomites, Northern Italy

8. Beautiful fern fossil found in Potsville Formation from Pennsylvania.
The ferns most commonly found are Alethopteris, Neuropteris, Pecopteris, and Sphenophyllum.

Image Credits: Kurt Jaccoud

9. Snowball garnet in schist

Syn-kinematic crystals in which “Snowball garnet” with highly rotated spiral Si. 

Porphyroblast is ~ 5 mm in diameter.
From Yardley et al. (1990) Atlas of Metamorphic Rocks and their Textures.

10. Trilobite Specimen from Wheeler Formation, Utah
The Wheeler Shale is of Cambrian age and is a world famous locality for prolific trilobite remains. 

Image Credits: Paleo Fossils


Correlation of Strata

The need to classify and organize rock layers according to relative age led to the geologic discipline of stratigraphy.

Rocks at different locations on Earth give different "snapshots" of the geologic time column.  At a particular location, the rocks never fully represent the entire geologic rock column due to extensive erosion or periods of non-deposition or erosion.

The thickness of a particular rock layer (representing a particular time period) will vary from one location to another or even disappear altogether.

The process that stratigraphers use to understand these relationships between strata at different localities is known as "correlation".

For example, rocks named Juras (for the Juras Mountains) in France and Switzerland were traced northward and found to overlie a group of rocks in Germany namedTrias.  The Trias rocks in turn, were found to underlie rocks named Cretaceous in England (the chalky “White Cliffs of Dover”).

Based on these relationships, is the Juras older or younger than the Cretaceous?  What are the two possible scenarios?

The location where a particular rock layer was discovered is called a "type locality".  Most of the “type localities” of the geologic time column are located in Europe because this is where the science of stratigraphic correlation started.

The Sedgwick/Murchison Debate

In 1835, Adam Sedgwick (Britain) and Roderick Murchison (Scotland) decided to name the entire succession of sedimentary rocks exposed throughout Europe.  They were geology colleagues and friends, but they had a famous argument over the division between the Cambrian and Silurian in Wales. 

Sedgwick’s topmost Cambrian overlapped with Murchison’s lowermost Silurian.  Eventually the disputed rock layers were assigned the age “Ordovician”.
Rocks Divisions versus Time Divisions

It is important to remember that the rock record is an incomplete representation of real geologic time due to the presence of unconformities.

Therefore, geologists are careful to distinguish geologic time from the rocks that represent snapshots of geologic time:


Examples: Precambrian/Phanerozoic


          Examples: Paleozoic/Cenozoic/Mesozoic


               Examples: Cambrian/Ordovician/Silurian

                    Formations (The main stratigraphic unit)

Rock divisions, such as the Cambrian System, can be correlated worldwide based on fossils.  In contrast, rock units such as groups, formations, and members are localized subsets of systems.  Rock units depend on the environment of deposition, which varies from one location to another.
Stratigraphic Rock Units

The rock divisions (Eonothem, Erathem, and System) simply divide rocks into the appropriate time eon, era, or period.  Obviously, all Cambrian System rocks are from the Cambrian regardless of their location on Earth's surface.

In contrast, the rock units (Groups, Formations, Members) are localized features (of limited regional extent) that depend on the local environment of deposition. 

The main rock unit of stratigraphy is the formation, a localized and distinctive (easily recognizable) geologic feature (i.e., the Chinle Formation of Late Triassic lake and river deposits in Arizona, Nevada, Utah, and New Mexico).

Different formations are distinguished and correlated based upon lithology (overall rock characteristics), which includes:

1) Composition of mineral grains
2) Color
3) Texture (grain size, sedimentary structures)
4) Fossils

Formations are “clumped” into groups and divided into members.

Datum- In correlation, a datum is a line of equivalent age.

The ideal datum is a stratigraphic marker that is both geographically extensive and represents an instantaneous moment in geologic time.  A good example is a volcanic ash layer that formed by a specific volcanic eruption followed by worldwide dispersal by atmospheric currrents.
Using Fossils for Strata Correlation

Sedimentary rocks that date from the same age can be correlated over long distances with the help of fossils.

Principle of Fossil Correlation- Strata containing similar collections of fossils (called fossil assemblages) are of similar age.  Also, fossils at the bottom of the strata are older than fossils closer to the top of the strata.

Index Fossils- Index fossils are the main type of fossil used in correlation.  To be an index fossil, a fossil species must be:

1) Easily recognized (unique).
2) Widespread in occurrence from one location to another.
3) Restricted to a limited thickness of strata (limited in age range).

The limited life-spans of these organisms allows us to easily constrain the age of rocks in which they occur.

The best index fossils are those that are free floating and independent of a particular sedimentary environment.  For example, organisms that are attached to one particular type of sediment are going to have limited geographic extent and will not be found in many rock types.   By contrast, organisms that are “free floaters” or “swimmers” will have a wider geographic extent and be found in many different rock types (i.e., trilobites).

fossil zone is an interval of strata characterized by a distinctive index fossil.

Fossil zones typically represent packets of 500,000 to 2,000,000 years.  Fossil zones boundaries do not have to correlate with rock formation boundaries.  Fossil zones may be restricted to a small portion of a formation or they may span more than one formation.

A fundamental assumption in fossil correlation is that once a species goes extinct, it will never reappear in the rock record at a later time.

Fossil types that are generally restricted to just one type of sediment are called facies fossils.  They are not very useful in correlation, but are extremely useful for reconstructing paleoenvironments.
  What is a Fossil?

Some examples of fossils are:

1) The preservation of entire organisms or body parts.  This includes the preservation of actual body parts (mammoths in tundra), as well as morphological preservation via the replacement of biological matter by minerals (petrified wood).
A petrified log in Petrified Forest National Park, Arizona, U.S.A.-impressions

2) Casts or impressions of organisms.
Eocene fossil fish Priscacara liops from Green River Formation of Utah

3) Tracks.
Trackways from ''Climactichnites'' (probably a slug-like animal), in the Late Cambrian of central Wisconsin.

4) Burrows.
Thalassinoides, burrows produced by crustaceans, from the Middle Jurassic of southern Israel.

5) Fecal matter (called coprolites).
Carnivorous dinosaur dung found in southwestern Saskatchewan,  USGS Image.
Theories on The Origin of Fossils

At one time, fossils were considered to be younger than the rocks in which they occurred.  People speculated that fossils formed when animals crawled into preexisting rock, died, and became preserved in stone.

Some people interpreted the widespread occurrence of fossilized marine organisms on land as support for a world-wide flood as described in scripture.

Leonardo da Vinci’s (1452 - 1519) Interpretation of Fossils
Self-portrait of Leonardo da Vinci, circa 1512-1515.

Regarding fossils that occur in strata many miles from the sea, da Vinci argued that:

1) The fossils could not have been washed in during a "Great Deluge" because they could not have traveled hundreds of miles in just 40 days.

2) The unbroken nature of the fossils suggest that they were not transported by violent water; instead the fossils represent formerly living communities of organisms that were preserved in situ.

3) The presence of fossil-rich strata separated by fossil-poor strata suggests that the fossils were not the result of a single worldwide flood, but formed during many separate events.
Lateral Variations in Formations

Historically, geologists initially believed that the layer-cake sequence of sedimentary rocks existed worldwide (i.e., that the layers extended indefinitely without change).

By the late 1700’s people began to realize that formations had a limited extent both vertically (up and down) and laterally (horizontally across Earth's surface).

People also began to realize that lithologic variations (changes in texture, color, fossils, etc) can occur laterally within formations themselves.

Today we interpret such variations in the context of modern depositional environments.  For example:



Near shore marine- The energy is high due to rough waters at the water-land interface.

Coarse sediments, and fossils of robust organisms that can withstand high energy environments.

Deep ocean- The energy is low due to the general calmness of water away from land.

Fine sediments, and fossils of more fragile organisms.

Note that the two different lithologies can be deposited simultaneously (representing the same moment in geological time) so long as they are deposited at different locations.

Different lithologies grade laterally into one another in a manner called intertonging.  An example is the way that the Old Red Sandstone of Wales (a terrestrial deposit) grades laterally into marine sediments of Devonshire to the south (both are Devonian).

Intertonging reflects the changes in depositional environments that occur over space and time (lateral and temporal variations).  Often these changes in environment are linked to shoreline migrations resulting from sea-level changes over time.
 Depositional Environments and Sedimentary Facies

Depositonal environments are characterized initially by the sediments that accumulate within them, and ultimately by the sedimentary rock types that form.  For example, a reef environment is characterized by carbonate reef-building organisms.  Ultimately, the sediments become lithified to form fossiliferous limestone.

sedimentary facies is a three-dimensional body of sediment (or rock) that contains lithologies representative of a particular depositional environment.  For example,




Mudstone and shale with interbedded sandstone.

Ocean basin

Laminated pelagic clays, cherts, and possible limestone.


Well-sorted, well-rounded, and possibly cross-bedded sandstone.

Analysis of sedimentary facies helps geologists to reconstruct past geologic environments and paleogeography.
Transgressions vs. Regressions

The sea-level has fluctuated throughout geologic history, and these changes have a profound effect on the geologic rock record.

transgression is an advance of the sea over land.

regression is a retreat of the sea from land area.

A transgressive facies pattern is characterized by:

1. The movement of marine facies landward over terrestrial facies.
2. A fining-upward sequence (the new marine environment is lower energy than the prior terrestrial environment).
3. A basal, erosional unconformity (erosion was more profound before the seas advanced).

A regressive facies pattern is characterized by:

1. The movement of terrestrial facies seaward and over marine facies.
2. A coarsening-upward sequence.
3. An erosional unconformity at the top.

Walther’s Law- Over time, the lateral changes in sedimentary facies due to transgressions and regressions will also produce vertical changes in sedimentary facies:

1. A transgressive facies sequence fines in the direction of the transgression, and also fines upward.
2. A regressive facies sequence coarsens in the direction of the regression, and also coarsens upward.

What causes transgressions and regressions?

1. Worldwide rises and falls in sea level (eustatic changes), perhaps related to climatic change.
2. Tectonic uplift, isostatic rebound, or crustal subsidence.
3. Rapid sedimentation.

It is often difficult or impossible to determine the exact cause of a transgression or regression seen in the geologic record.  The cause may be worldwide or local.  The fact that there is a transgression or regression indicates an “apparent” sea-level change.
 The Stratigraphy of Unconformities

Recall that unconformities represent missing time due to:

1)      Periods of non-deposition.
2)      Periods of erosion.

The main types of unconformities are:
1. Disconformity
2. Angular unconformity
3. Nonconformity
4. Paraconformity

Unconformities vary from one location to another (just like rock formations and sedimentary facies).  In other words, some locations along the unconformity surface will represent more missing geologic time than others.

Unconformities may eventually disappear laterally and transition into a conformable sequence of strata.

Oil companies use large scale, unconformity bounded rock units called sequences to correlate rocks in a process called sequence stratigraphy.

Six major unconformity-bounded sequences are recognized worldwide in the Phanerozoic.  These sequences are not restricted to period or era boundaries.

The major sequences are believed to represent worldwide fluctuations in sea-level.

Stratigraphy: Making sense of chaos

What is Stratigraphy?

Stratigraphy- The branch of geology that seeks to understand the geometric relationships between different rock layers (called strata), and to interpret the history represented by these rock layers.

Public Domain Image by the US Dept. of Interior.

Contact- A boundary that separates different strata or rock units.
Steno's Laws of Stratigraphy

Image from J. P. Trap: berømte danske mænd og kvinder, 1868

Nicholas Steno (1638-1686) was a Danish-born pioneer of geology, and is considered to be the father of stratigraphy.

Nicholas Steno's observations of rocks layers suggested that geology is not totally chaotic.  Rather, the rock layers preserve a chronological record of Earth history and past life.

He developed three fundamental principles of stratigraphy, now known as Steno's Laws:

1) Law of Original Horizontality– Beds of sediment deposited in water form as horizontal (or nearly horizontal) layers due to gravitational settling.

2) Law of Superposition– In undisturbed strata, the oldest layer lies at the bottom and the youngest layer lies at the top.

3) Law of Lateral Continuity– Horizontal strata extend laterally until they thin to zero thickness (pinch out) at the edge of their basin of deposition.
Other Important Principles of Stratigraphy

4) Law of Cross-Cutting Relationships– An event that cuts across existing rock is younger than that disturbed rock.  This law was developed by Charles Lyell (1797-1875).

5) Principle of Inclusion– Fragments of rock that are contained (or included) within a host rock are older than the host rock.
Unconformity – A surface that represents a very significant gap in the geologic rock record (due to erosion or long periods of non-deposition).
There are 3 main types of unconformities:
1) Disconformity – A contact representing missing rock between sedimentary layers that are parallel to each other.  Since disconformities are parallel to bedding planes, they are difficult to see in nature.

2) Angular Unconformity – A contact in which younger strata overlie an erosional surface on tilted or folded rock layers.  This type of unconformity is easy to identify in nature.
Image provided by FCIT. Original image from Textbook of Geology by Sir Archibald Geikie (1893).
3) Nonconformity – A contact in which an erosion surface on plutonic or metamorphic rock has been covered by younger sedimentary or volcanic rock.
4) Paraconformity- A contact between parallel layers formed by extended periods of non-deposition (as opposed to being formed by erosion).  These are sometimes called "pseudo unconformities").
Unconformities VS Bedding Planes
Unconformities represent huge gaps in time!  The nonconformity between the Vishnu Schist and overlying sedimentary layers in the Grand Canyon represents 1.3 billion years of missing rock record.
Bedding planes, or planes separating adjacent sedimentary layers, also represent gaps in the rock record but on a much smaller scale than an unconformity.
Relative Age Dating
Relative age dating is a way to use geometric relationships between rock bodies to determine the sequence of geologic events in an area.  Relative dating is different from absolute dating in which specific dates are assigned to geologic events (we will discuss absolute dating techniques later).
Relative dating is based on the five principles of stratigraphy discussed above.
Historical Perspective on the Origin of Rocks: Werner's Concept of Neptunism

Abraham Werner (1749-1817), a German geologist, proposed that Earth’s crust originated in ocean water through the process of precipitation.  This idea became known as Neptunism, in reference to the Roman God of the sea.

Werner classified rocks into 4 categories, as shown in the diagram below:

Figure by RJR

1. Primitive rock (red)– Granite and metamorphic rock were precipitated from oceans.

2. Transition rock (light brown)– Next, fossil-rich sedimentary rocks were precipitated.  These rocks are tilted due to deposition on the non-horizontal surfaces of primitive rocks.  This aspect of Werner's model was useful for explaining the origin of tilted sedimentary rocks.

3. Secondary rock (dark brown)– Flat lying sedimentary rocks were eventually precipitated.  The secondary rocks were thought to include interlayered basalts, which Werner thought formed by combustion of buried coal layers.

4. Tertiary (or alluvial) rock (yellow)– Finally, after the ocean receded, recent erosion and deposition created a thin veneer of overlying sediment.

Today we know that Werner's basic assumption that granite precipitated from seawater is incorrect.  We also know that basalt is not the product of coal combustion.

Nevertheless, Werner's concept of Neptunism was influential because:

1) Werener was right that some sedimentary rocks, such as limestones, do precipitate from ocean water.

2) Werner was not a catastrophist and did not need to make his interpretation of rock layers consistent with scriptual teachings.

3) Werner’s relative age assignments represents an early attempt to determine Earth's sequential history.
Historical Perspective on the Origin of Rocks: Hutton's Concept of Plutonism

The Scottish geologist James Hutton (1726-1797) argued that granite and basalt by solidification within the earth (as opposed to precipitating in from oceanwater).  This idea is known as Plutonism, in reference to the God of the deep underworld.

This concept of plutonism was supported by basalt melting/cooling experiments Sir James Hall conducted in 1792.  These experiments showed that the basalts form by the solidification of liquid magma.

Hutton viewed tilted strata as having been initially deposited horizontally, and then were subsequently deformed (tilted and folded) by the forces of Earth's internal heat engine.  He would argue that these forces gave rise to mountains.

Furthermore, he suggested that the mountains eroded to produce the sedimentary rocks we find in the rock record.

Hutton viewed the earth continually recycling itself with a balance between destruction and rejuvenation.  Mountains are created, eroded, and reformed.

Hutton’s ideas were not well received by people in the early 1800’s because he was a poor writer, and because his science was anti-catastrophic and did not support the scriptures.

Carbonate diagenesis

Cements in carbonate rocks are mainly made up of calcium carbonate derived from the host sediment. Lithification of aggregates of carbonate material can occur as eogenetic cementation contemporaneously with deposition in any settings where there is either a lot of seawater being circulated through the sediment or where sedimentation rates are low. Beach-rock may be formed of carbonate debris deposited on the beach that is cemented by calcium carbonate from seawater washing through it in the intertidal to supratidal zone. In warm tropical shallow marine environments the seawater is often saturated with respect to calcium carbonate and cementation can take place on the sea floor forming a hardground or firmground if sedimentation rates are low. The cementation can be localised and related to microbial activity within the sediment, for example, it may be associated with burrows. Colder seawater is undersaturated with calcium carbonate and dissolution of carbonate material can occur. In non-marine environments calcite cementation occurs in both the vadose zone (above the water table) and in the phreatic zone (below the water table). In the vadose environment, for example in caves and in streams, the precipitation of the calcite to form these cements is due to the degassing of water: the resulting deposits are stalactites and stalagmites in caves (or speleothems, the general term for cave deposits), and travertine deposited from surface waters in places such as waterfalls. In soils calcite precipitation forms cements as rhizoliths and calcrete as a result of the evaporation of groundwater and the addition of calcium carbonate as wind-blown dust. Syn-sedimentary precipitation of siderite can occur where there is mixing of seawater and fresh water under reducing conditions: this can happen in coastal marshes. Burial stage (mesogenetic) cementation by calcite largely involves carbonate derived from the dissolution of carbonate grains. These cements are low magnesium calcite and are in the form of bladed crystals that grow out from the grain margins into the pore spaces or as overgrowths, particularly on crystalline fragments of echinoids and crinoids, from which they may develop a poikilotopic fabric.

Compaction effects in limestones: stylolites and bedding planes

Calcite undergoes pressure dissolution under the pressure of a few hundred metres of overburden, forming solution surfaces within the rock known as stylolites. At a small scale (millimetres to centimetres), stylolites are usually highly irregular solution surfaces that are picked out by concentrations of clay, iron oxides or other insoluble components of the rock. Where a stylolite cuts through a fossil it may be possible to determine the amount of calcium carbonate that has been dissolved at the surface. They normally form horizontally in response to overburden pressure, but can also form in response to tectonic pressures at high angles to the bedding. At a larger scale, horizontal pressure solution surfaces within a limestone succession create apparent bedding surfaces that may be very sharply defined by the higher concentration of clay along the surface, but do not necessarily represent a break in sedimentation. This apparent bedding, which is diagenetic in origin, may be more sharply defined in outcrop than true bedding surfaces representing primary changes and breaks in deposition. Pressure solution can result in the removal of large amounts of calcium carbonate and concentrate the clay component of an impure, muddy limestone to leave nodules of limestone in a wavy-bedded mudstone.


Dolomite is a calcium magnesium carbonate (CaMg (CO3)2) mineral that is found in carbonate sedimentary rocks of all ages and when the mineral forms more than 75% of the rock it is called a dolostone, although the term dolomite is also often used for the rock as well as for the mineral. The mineral is relatively uncommon in modern depositional environments: it is known to occur in small quantities in arid coastal settings, where its formation may be related to microbial activity. However, these modern examples do not provide an explanation for the thick successions of dolostone that are known from the stratigraphic record and most dolomite is believed to form diagenetically, a process known as dolomitisation. Many dolostones in the stratigraphic record contain fossils that indicate normal marine environments of deposition and show replacement fabrics where material that was clearly originally made up of calcite or aragonite has been wholly or partially replaced by dolomite. The mechanism of formation of dolomite by reaction of seawater and pore water with calcite and aragonite has been the subject of much debate and a number of different models have been proposed, all of which may be applicable in different circumstances. All models have certain things in common: the original rock must be limestone, the water that reacts with it must be marine, or pore water derived from seawater, and there must be abundant, long-term supply of those waters for large-scale dolomitisation to take place. The process of dolomitisation also seems to be favoured by elevated temperatures and by either enhanced or reduced salinities compared with seawater. The mixing-zone model for dolomitisation proposes that where fresh water, which is under-saturated with respect to calcite but over-saturated with respect to dolomite, mixes with marine waters then dolomitisation would occur. Although there may be a theoretical basis for this model, the process has not been observed in any of the many coastal regions around the world where conditions should be favourable. Arid coastal regions where concentrated brines promote dolomitisation have been suggested in the reflux model, but although this may result in formation of dolomite in the sediment within 1 or 2m of the surface, this mechanism does not seem to be capable of generating large volumes of dolomite. It seems more likely that large-scale dolomitisation occurs at some point after burial and hence a number of burial models or seawater models have been proposed. Thick successions of platform limestone can be transformed wholly or partly into dolostone if seawater, or pore-water brines that originated as seawater, can be made to pass through the rock in large quantities for long periods of time. Compaction has been suggested as a potential driving force for fluid transport, but seems unlikely to be capable of producing the quantities of fluids required. Thermally driven circulation, either by a geothermal heat source or by temperature differences between the interior of a platform and seawater, is the most likely candidate for generating long-term flow of the large quantities of fluid required. Topography can also provide a means of forcing water flow through rocks, but although meteoric waters (i.e. derived from rainfall) may provide an abundant flux of fluids, they rarely contain sufficient magnesium to promote dolomitisation. A reversal of the process that causes dolomitisation in association with evaporites can result in dolomite being replaced by calcite. This dedolomitisation occurs where beds of gypsum are dissolved enriching groundwaters in calcium sulphate. The sulphate-rich waters passing through dolostone result in the replacement of dolomite by calcite.

Diagenesis and carbonate petrography

Most carbonate sediments become lithified during diagenesis and can readily be cut to make thinsections: injection of blue resin into the pore spaces is nevertheless commonly carried out in order to make any voids within the rock visible. The blue-dyed resin shows up porosity in carbonate rocks that can either be between the grains (interparticle porosity) or within grains as intraparticle porosity, usually chambers within fossils such as foraminifers, cephalopods and gastropods. Distinguishing between cement and matrix and even between grains and cement is not always straightforward in carbonate rocks because all have the same, or very similar, mineralogy: the morphology of the carbonate material therefore provides most of the important clues as to its origin. Grains within limestone that are biogenic in origin usually have distinctive shapes that reflect the structure of the organism, even if they are only small fragments. Similarly, ooids and peloids are easily recognised in thin-sections. Lithic clasts of limestone and intraclasts have more variable shapes and structures and, because they are in fact pieces of rock, may include areas of cement: distinguishing between the cement within intraclasts and the later cement of the whole rock can sometimes be difficult. Peloids are typically made up of carbonate mud, and must therefore be distinguished from a muddy matrix on the basis of their shape.


Carbonate mud is the main constituent of carbonate mudstones and wackestones, and can occur as a
matrix in packstones, grainstones and boundstones. Individual grains are clay-sized and therefore cannot be individually seen with a petrographic microscope. Neomorphism (replacement by recystallisation) of carbonate mud to form microcrystalline sparry calcite commonly occurs, and as this results in an increase in crystal size, it may then be possible to see the crystalline form under the microscope: although it may be difficult to resolve individual crystals, the microspar appears as a mass of fine crystalline materials showing different birefringence colours under crossed polars. The birefringence colours of carbonates are high-order pink and green, which may appear to merge into a pale brown if the individual crystals are very small or the magnification is low. Shelly or skeletal material composed of aragonite undergoes replacement by calcite, either by the solution of the aragonite to create a void later filled by calcite, or by a direct mineral replacement. In the former case the internal structure is completely lost, but where the aragonite is transformed into calcite some relics of the original internal structure may be retained, seen as inclusions of organic matter. The neomorphic calcite crystals are larger than the original aragonite crystals, are often slightly brown due to the presence of the organic material and occur as an irregular mosaic occupying the external form of the skeletal material.

Carbonate cements

Cementation ofcarbonate sediment to form a limestone can involve a number of stages of cement formation. The form of eogenetic cements is determined by the position of the sediment relative to the groundwater level. In the phreatic zone, in which all the pore spaces are filled with water, the first stage is the formation of a thin fringe of calcite or aragonite growing perpendicular to the grain boundary out into the pore space: these crystals form a thin layer of approximately equal thickness over the grains and are hence known as isopachous cement. Above the water level, in the intertidal and supratidal zones, the sediment is in the vadose zone and is only periodically saturated with water: the cement forms only where grains are close together within water held by surface tension to form a meniscus, and hence they are called meniscus cements. A bladed, fibrous or acicular morphology is characteristic of these early cements, with the long axes of the crystals oriented perpendicular to the grain edge. Very fine-grained, micritic, cements can also form at this stage. Recrystallisation of these eogenetic cements commonly occurs because if their original mineralogy was either aragonite or high-magnesium calcite they undergo change to low magnesium calcite through time. Many limestones have a cement of sparry calcite that fills in any pore space that is not occupied by an early cement. The interlocking crystals of clear calcite are believed to form during burial diagenesis (mesogenetic cement) from pore waters rich in calcium carbonate. If there are fragments of echinoids or crinoids present in the sediment the sparry cement precipitates as a syntaxial overgrowth and can form poikilotopic fabric as the cement crystals completely envelop a number of grains. The source of the calcium carbonate for these sparry cements may be from the dissolution of aragonite from shelly material or it may come from pressure solution at grain contacts and along stylolites.


Most dolomite occurring in sedimentary rocks is diagenetic in origin, occurring as a replacement of calcite. Although the optical properties of calcite and dolomite are very similar, dolomite commonly occurs as distinctive, small rhomb-shaped crystals that replace the original calcite fabric. Staining the thin section with Alizarin Red-S provides confirmation that the mineral is dolomite (which does not stain pink) as opposed to calcite (which does). Extensive dolomitisation may completely obliterate the primary fabric of the limestone, resulting in a rock that appears in thin-section as a mass of rhombic crystals. The transformation of calcite into dolomite results in a decrease in mineral volume and consequently an increase in porosity.

Chemical processes of diagenesis

A certain amount of modification of the sediment occurs at the sediment–water and sediment–air interfaces: cements formed at this stage are referred to as eogenetic cements and they are essentially synsedimentary, or very soon after deposition. Most chemical changes occur in sediment that is buried and saturated with pore waters, and cements formed at this stage are called mesogenetic. Rarely cement formation occurs during uplift, known as telogenetic cementation. During these diagenetic stages, chemical reactions take place between the grains, the water and ions dissolved in the pore waters: these reactions take place at low temperatures and are generally very slow. They involve dissolution of some mineral grains, the precipitation of new minerals, the recrystallisation of minerals and the replacement of one mineral by another.


The processes of grain dissolution are determined by the composition of the grain minerals and the chemistry of the pore waters. Carbonate solubility increases with decreasing temperature and increasing acidity (decreasing pH): the presence of carbon dioxide in solution will increase the acidity of pore waters and leaching of compounds from organic matter may also reduce the pH. It is therefore common for calcareous shelly debris within terrigenous clastic sediment to be dissolved, and if this happens before any lithification occurs then all traces of the fossil may be lost. Dissolution of a fossil after cementation may leave the mould of it, which may either remain as a void or may subsequently be filled by cement to create a cast of the fossil. Silica solubility in water is very low compared with calcium carbonate, so large-scale dissolution of quartz is very uncommon. Silica is, however, more soluble in warmer water and under more alkaline (higher pH) conditions, and opaline silica is more soluble than crystalline quartz. Most quartz dissolution occurs at grain boundaries as a pressure dissolution effect, but the silica released is usually precipitated in adjacent pore spaces.

Precipitation of cements

The nucleation and growth of crystals within pore spaces in sediments is the process of cementation. A distinction must be made between matrix, which is fine-grained material deposited with the larger grains, and cements, which are minerals precipitated within pore spaces during diagenesis. A number of different minerals can form cements, the most common being silica, usually as quartz but occasionally as chalcedony, carbonates, typically calcite but aragonite, dolomite and siderite cements are also known, and clay minerals. The type of cement formed in a sediment body depends on the availability of different minerals in pore waters, the temperature and the acidity of the pore waters. Carbonate minerals may precipitate as cements if the temperature rises or the acidity decreases, and silica cementation occurs under increased acidity or cooler conditions. Growth of cement preferentially takes place on a grain of the same composition, so, for example, silica cement more readily forms on a quartz grain than on grains of a different mineral. Where the crystal in the cement grows on an existing grain it creates an overgrowth with the grain and the cement forms a continuous mineral crystal. These are referred to as syntaxial overgrowths. Overgrowths are commonly seen in silica-cemented quartz sands; thin-section examination reveals the shape of a quartz crystal formed around a detrital quartz grain, with the shape of the original grain picked out by a slightly darker rim within the new crystal. In carbonate rocks overgrowths of sparry calcite form over biogenic fragments of organisms such as crinoids and echinoids that are made up of single calcite crystals. Cementation lithifies the sediment into a rock and as it does so it reduces both the porosity and the permeability. The porosity of a rock is the proportion of its volume that is not occupied by solid material but is instead filled with a gas or liquid. Primary porosity is formed at the time of deposition and is made up mainly of the spaces between grains, or interparticle porosity, with some sediments also possessing intraparticle porosity formed by voids within grains, usually within the structures of shelly organisms. Cements form around the edges of grains and grow out into the pore spaces reducing the porosity. Secondary porosity forms after deposition and is a result of diagenetic processes: most commonly this occurs as pore waters selectively dissolve parts of the rock such as shells made of calcium carbonate. Permeability is the ease with which a fluid can pass through a volume of a rock and is only partly related to porosity. It is possible for a rock to have a high porosity but a low permeability if most of the pore spaces are not connected to each other: this can occur in a porous sandstone which develops a partial cement that blocks the 'throats' between interparticle pore spaces, or a limestone that has porosity sealed inside the chambers of shelly fossils. A rock can also have relatively low porosity but be very permeable if it contains large numbers of interconnected cracks. Cement growth tends to block up the gaps between the grains reducing the permeability. Pore spaces can be completely filled by cement resulting in a complete lithification of the sediment and a reduction of the porosity and permeability to zero.


The in situ formation of new crystal structures while retaining the basic chemical composition is the process of recrystallisation. This is common in carbonates of biogenic origin because the mineral forms created by an organism, such as aragonite or high magnesium calcite, are not stable under diagenetic conditions and they recrystallise to form grains of low magnesium calcite. The recrystallised grains will commonly have the same external morphology as the original shell or skeletal material, but the internal microstructure may be lost in the process. Recrystallisation occurs in many molluscs, but does not occur under diagenetic conditions in groups such as crinoids, echinoids and most brachiopods, all of which have hard parts composed of low magnesium calcite. Recrystallisation of the siliceous hard parts of organisms such as sponges and radiolaria occurs because the original structures are in the form of amorphous opaline silica, which recystallises to microcrystalline quartz.


The replacement of a grain by a different mineral occurs with grains of biogenic origin and also detrital mineral grains. For example, feldspars are common detrital grains and to varying degrees all types of feldspar undergo breakdown during diagenesis. The chemical reactions involve the formation of new clay minerals that may completely replace the volume of the original feldspar grain. Feldspars rich in calcium are the most susceptible to alteration and replacement by clay minerals, whereas sodium-rich, and particularly potassium-rich, feldspars are more resistant. These reactions may take millions of years to complete. Silicification is a replacement process that occurs in carbonate rocks: differences between the mineralogy of a shelly fossil and the surrounding carbonate rock may allow the calcium carbonate of the fossil to be partly or completely replaced by silica if there are silica-rich pore waters present in the rock.

Nodules and concretions

Most sedimentary deposits are heterogeneous, with variations in the concentrations of different gain sizes and grain compositions occurring at all scales. The passage of pore waters through the sediment will be affected by variations in the porosity and permeability due to the distribution of clay particles that inhibit the flow. The presence of the remains of plants and animals creates localised concentrations of organic material that influence biochemical reactions within the sediment. These heterogeneities in the body mean that the processes that cause cementation are unevenly dispersed and hence some parts become cemented more quickly than others. Where the distinction between well-indurated patches of sediment and the surrounding body of material is very marked the cementation forms nodules and concretions. Irregular cemented patches are normally referred to as nodules and more symmetrical, round or discoid features are called concretions. Nodules and concretions can form in any sediment that is porous and permeable. They are commonly seen in sand beds (where large nodules are sometimes referred to as doggers), mudrock and limestone. Sometimes they may be seen to have nucleated around a specific feature, such as the body of a dead animal or plant debris, but in other cases there is no obvious reason for the localised cementation. Concretions formed at particular levels within a succession may coalesce to form bands of well-cemented rock. A variety of different minerals can be the cementing medium, including calcite, siderite, pyrite and silica. In places there is clear evidence that concretions in mudrocks form very soon after deposition: if the layering within the mudstones drapes around the concretion. This is evidence that the cementation occurred locally before the rock as a whole underwent compaction.

Septarian concretions

The interiors of some carbonate concretions in mudstones display an array of cracks that are often filled with sparry calcite. These are known as septarian structures, and they are believed to form during the early stages of burial of the sediment. The precise mechanism of formation of the cracks is unclear, but is believed to be either the result of shrinkage (in a process similar to syneresis), or related to excess pore fluid pressure in the concretion during compaction, or a combination of the two.

Flints and other secondary cherts

Chert can form directly from siliceous ooze deposited on the sea floor: these primary cherts occur in layers associated with other deep-water sediments. Chert may also form in concretions or nodules as a result of the concentration of silica during diagenesis. These secondary cherts are diagenetically formed and are common in sedimentary rocks, particularly limestones. They are generally in the form of nodules that are sometimes coalesced to form layers. The diagenetic origin to these cherts can be seen in replacement fabrics, where the structures of organisms that originally had carbonate hard parts can be seen within the chert nodules. The edges of a chert nodule may also cut across sedimentary layering. The nodules form by the very fine-scale dissolution of the original material and precipitation of silica, often allowing detailed original biogenic structures to be seen. The source of the silica is generally the remains of siliceous organisms deposited with the calcareous sediment. These organisms are sponges, diatoms and radiolarians that originally have silica in a hydrated, opaline form, and in shelf sediments sponge spicules are the most important sources of silica. The opaline silica is relatively soluble and it is transported through pore waters to places where it precipitates, usually around fossils, or burrows as microcrystalline or chalcedonic quartz in the form of a nodule. Flint is the specific name given to nodules of chert formed in the Cretaceous Chalk.

Colour changes during diagenesis

The colour of a sedimentary rock can be very misleading when interpretation of the depositional environment is being attempted. It is very tempting to assume, for example, that all strongly reddened sandstone beds have been deposited in a strongly oxidising environment such as a desert. Although an arid continental setting will result in oxidation of iron oxides in the sediment, changes in the oxidation state of iron minerals, the main contributors to sediment colour, can occur during diagenesis. A body of sediment may be deposited in a reducing environment but if the pore waters passing through the rock long after deposition are oxidising then any iron minerals are likely to be altered to iron oxides. Conversely, reducing pore waters may change the colour of the sediment from red to green. Diagenetic colour changes are obvious where the boundaries between the areas of different colour are not related to primary bedding structures. In fine grained sediments reduction spots may form around particles of organic matter: the breakdown of the organic matter draws oxygen ions from the surrounding material and results in a localised reduction of oxides from a red or purple colour to grey or green. Bands of colour formed by concentrations of iron oxides in irregular layers within a rock are called liesegangen bands. The bands are millimetre-scale and can look very much like sedimentary laminae. They can be distinguished from primary structures as they cut across bedding planes or cross-strata and there is no grain-size variation between the layers of liesegangen bands. They form by precipitation of iron oxides out of pore waters. Other colour changes may result from the formation of minerals such as zeolites, which are much paler than the dark volcanic rocks within which they form.