Biological and Chemical Sedimentary Rock


These are sedimentary rocks that have been precipitated out of solution, either by physical processes (as described in the previous notes), or more commonly as the result of biolgical activity - particularly the construction of skeletal parts.
The most important types of these rocks, as defined by composition, are calcium carbonate and other carbonates, silica, and deposits of sodium chloride and gypsum.

Carbonate Rocks


These are mostly calcium carbonate (CaCO3) (calcite and aragonite). Dolomite is also an abundant mineral. Less abundant are copper and iron carbonates.

Carbonate minerals form from the reaction of carbon dioxide in the atmosphere with water in the oceans.

1) CO2(g) <===> CO2(aq)
2) CO2(aq) + H2O(l) <===> H2CO3(aq)
3) H2CO3(aq) <===> H1+ + HCO31-(aq)
4) HCO31-(aq) <===> H1+ + CO32-(aq)
5) Ca2+(aq) + CO32-(aq) <===> CaCO3(s)

(double arrows are used as each of these reactions represents an equilibrium system rather than a one-way reaction)

The source of calcium ions is the weathering of volcanic rocks.

The ultimate source of the carbon dioxide at the earth's surface seems to be from volcanic emissions. In other words, from the mantle. There is evidence of carbon, carbon dioxide, and carbonate minerals in asteroids and comets (as well as neighbouring planets), but I have not seen any indication of how much these sources contributed to the carbon supply on the earth since it was formed in the early solar system.

From what I have been able to gather, of all the carbon on the earth, 94% or so is in the mantle, 5% is found as carbonate minerals in the lithosphere, and 1% as organic carbon deposits (fossil fuels and their precursor molecules (called kerogens). The carbon in the biosphere, hydrosphere, and atmosphere amount to less than 0.1% of the total.
The following chart gives the amounts of carbon (in Gigatonnes) stored in various forms in the lithosphere, hydroshpere, atmosphere, and biosphere. Note that these figures are massses of carbon. Carbon dioxide is only 27.3% carbon, so you would have to multiply each number by about 4 to get masses of carbon dioxide.


We also have measured the rate at which carbon is transferred between these "sinks" as follows:


The fluxes (transfers between sinks) described in the diagram above comprise what we call the fast carbon cycle. There is a much slower exchange of carbon between the fast cycle and the carbon trapped in carbonate sedimentary rock and the mantle. The rate at which carbon is cycled back into the mantle by subduction at convergent plate boundaries and back into the atmosphere through volcanic activity is about 100 times slower than the rate at which carbon is added to the atmosphere by human activities. The slow carbon cycle may or may not be in long-term equilibrium (cycled into the rock as fast as it is cycled out). There is evidence that carbon dioxide levels were much higher in the geological past (100s of millions of years ago. Over the short term, we are definitely not at equilibrium within the fast cycle.

Calcium Carbonate Chemistry

Calcium carbonate is precipitated by biological activity and by some physical processes. The low solubility of calcium carbonate and the abundance of the two ions makes it an ideal mineral for skeletons. Most of the shallow oceans are close to saturated with respect to this mineral, so it is easy for organisms to precipitate it.

CaCO3 solubility:
  1. decreases with increasing temperature (by a factor of 4 from OoC to 100oC),
  2. increases with increasing pressure
  3. increases with increasing acidity (decreasing pH)
  4. increases with increasing dissolved carbon dioxide concentration (principally because this decreases pH)
Point 3 results from the fact that excess hydrogen ions causes reaction 4 (near the top of the page) to shift in reverse (using up carbonate and hydrogen ions to make bicarbonate ions).
Point 4 results from the production of carbonic acid (reaction 2) which ionizes to make hydrogen ions and bicarbonate ion.

The result of these features of carbonate chemistry is that acid production by any means and the increase of dissolved carbon dioxide will tend to dissolve carbonate minerals.
Another result of this complex chemical equilibrium is that there is a depth at which the rate of calcium carbonate dissolition (dissolving) is greater than the rate at which it can accumulate. This is because decay of dead organisms in the deep ocean waters produces higher concentrations of dissolved carbon dioxide. The depth below which calcium carbonate cannot accumulate is called the carbonate compensation depth (CCD). In modern times, this occurs at a depth of about 4.5 km below the ocean surface. In deeper parts of the oceans, only silica sediments can accumulate.

Karst Topography
The dissolution of carbonate sedimentary rock also can take place on land where ground water or rain is acidic enought to dissolve away the calcium carbonate. This can form large cave systems and at the surface can form a topographic feature called karst: an extremely irregular surface caused by uneven dissolition of carbonate minerals.



Diagnostic Test
Another important consequence of carbonate chemistry is the diagnostic test for carbonate rock: its reaction with hydrochloric acid. Most carbonates react visibly (fizzing) when in contact with 10% HCl (about 1.2 M). Dolomite does not, unless it is powdered first, which is a useful distinguishing feature in of itself.

Calcium Carbonate Sediment

There are several major sources of carbonate sediment, all of which can form into limestone when cemented together.
One of the major differences between clastic and carbonate sediment is that because calcium carbonate is easier to dissolve and reprecipitate than silica, calcium carbonate sediments can lithify much sooner after deposition. Some carbonate sediment lithifies (gets cemented into a rock) right at the sediment surface with no need for deep burial.
Dolomite, calcium magnesium carbonate, is a more chemically resistant carbonate mineral that is thought to form as magnesium ion-rich water percolates through calcium carbonate sediments after burial.

1) Skeletal Debris from large organisms (Biological)
These organisms include bivalves (clams, a class of mollusc), brachiopods (similar to bivalves, but not related to molluscs at all and with a much different internal anatomy), crinoids (sea lilies) and other echinoderms (sand dollars, starfish, sea urchins), corals, and many others. Limestones from this material can be composed largely of skeletal pieces or small debris made from broken up skeletons.


2) Microfossil sediment (Biological)
The oceans are home to a wide diversity of different microscopic (many are single-celled organisms) animals and plants that secrete calcite and aragonite shells. The sedimentary rock known as chalk is made mostly of the skeletons of single celled algae called coccolithophores. They assemble a shell composed of overlapping oval plates called coccoliths. The were especially common in the Mesozoic Era. Forams are predetory amoeba-like organisms, also single-celled, that form spiral shells of many differenet shapes. They also contribute a major component of some limestones.




3) Micritic Lime Mud (Biological and chemical)
Micrite is a fine-grained mud that forms in shallow water from the disintegration of calcareous algae (algae that forms a calcium carbonate crust to protect it) as well as from direct preciptation from seawater. Micrite also can form from fecal material. Micrite often forms a part of the other classes of limestone mentioned here.
4) Ooid Sediment (Chemical)
Ooids are small, sand-sized spheres of calcium carbonate that are seen to form in shallow, tropical marine (ocean) environments. They are thought to form as small particles of carbonate debris are rolled around on the sediment surface by wave action. They often display concentric layering, like a hail stone. Sticky coatings of algae and bacteria may play a role in the build-up of the calcium carbonate material. When they are cemented together, the sedimentary rock is called a oolite.
4) Travertine and Speleothems (Chemical)
These forms of chemical precipitation of calcium carbonate occur when mineral rich water moving underground is exposed to the air releases dissolved carbon dioxide. This causes an decrease in the solubility of calcium carbonate (see above) which then precipitates out of solution.

Non-carbonate Sedimentary Rocks

Evaporites (Chemical).
The most common of these are sodium chloride and gypsum. They commonly form in what are called evaporite deposits.
They typically form in shallow water in warm climates. Restricted bodies of water where infrequent influx of new water (supplying new dissolved minerals) alternates with long periods of evaporation. In seawater, evaporation results in gypsum precipitation when about 80% of the water has evaporated, followed by precipitation of sodium chloride once 90% of the water has evaporated.

Silica (Biological and Chemical).
Diatomite is a sedimentary rock made from the compressed shells of diatoms (small algal cells). These shells fall to the ocean floor after the death of the cell and accumulate. This rock is prevalent in environments where calcium carbonate is not formed or accumulated. This material is especially valued for its utility as a filtering material for water purification and in the beverage industry.

Chert, micro-crystalline silica can form from silica that is dissolved and reprecipitated. The source of the silica can be diatoms or similar organisms or it can be from clastic sediments. Chert often forms nodules in other sediment. These nodules can merge, if they are abundant enough, to form distinct layers in other rocks, particularly limestones. The precipitation of these nodules results from local changes to the chemical environment in the fluids within sediment layers that causes silica solubility with in the pore fluids to decrease.


Crystalline silica can grow into void spaces forming geodes.

Coal (Biological).
Coal is formed when plant material is buried by sediment that locks it away from oxygen. As the plant matter is buried deeper, heat and pressure compress the organic matter and drive off most the organic molecules, leaving behind relatively pure carbon. Coal is an important fossil fuel source, although since it contains no hydrogen (unlike oil and natural gas) its combustion produces more carbon dioxide for a given amount of energy than other fossil fuels.