Fate of Organic Matter in Sedimentary Basins, Chemistry tutorial

Accumulation of Organic Matter:

Production, accumulation and preservation of the undegraded organic matter are prerequisites for the existence of petroleum. It must be noted that the word 'organic matter' doesn't comprise mineral skeletal parts, like shells, bones and teeth. The accumulation of organic matter in sediments is controlled via a number of geological boundary conditions. This is practically limited to sediment deposited in the aquatic environments that should get a certain minimum amount of organic matter. This organic matter can be supplied either in the form of dead or living particulate organic matter or as the dissolved organic matter. The organic material might be autochthonous to the environment where it is deposited, that is, it originated in the water column above or in the sediment in which it is buried, or it might be allochthonous, that is, foreign to its atmosphere of deposition. Both the energy situation in the water body in question and the supply of mineral sedimentary particles should be like to allow a specific type of sedimentation. If the energy level in a body of water is too high, either there is erosion of sediment instead of deposition or deposited sediment is too coarse to retain low-density organic material. An illustration is a beach area having strong wave action. Moreover, in coarse-grained sediment, ample diffusion of oxygen is possible via the wide open pores. On the other hand, if the level of energy is very low, too little sediment is supplied, and there is, similarly, no appreciable organic sedimentation. Illustrations of this kind take place in certain portions of the deep sea. 

Once such boundary conditions are satisfied, the accumulation of organic matter in sediment is based on the dualism between methods that conserve and concentrate and those that destroy and dilute organic matter.


Sediments deposited in the sub-aquatic environments have huge amounts of water (that is, the amount of water is 60% of the net weight of sediment), minerals, dead organic material and many living microorganisms. Such a mixture results from different sedimentary methods and primary components of very dissimilar origin it is not in equilibrium and thus unstable, even if the microorganisms are not present. Diagenesis is a method via which the system tends to   approach equilibrium under conditions of the shallow burial, and via which the sediment generally becomes consolidated. The depth interval concerned is in the order of some hundred meters, occasionally to some thousand meters. In early diagenetic method, the increase in temperature and pressure is small and the transformation of sediments takes place under mild conditions.

Throughout early diagenesis, microbial activity converts the sediment. Anaerobic organisms decrease sulphates to free oxygen; the oxygen so generated is consumed via aerobic microorganisms which live in the uppermost layer of sediments. The energy needed is given by the decomposition of organic matter, which in the process is transformed into carbon-dioxide, ammonia and water. The conversion is generally carried out fully in sands and partially in mud. Throughout this period, the Eh reduces abruptly and the pH increases slightly. Moreover, some solids such as CaCO3 and SiO2 dissolve and reach the saturation and re-precipitate, altogether with authigenic minerals like sulphides of iron, copper, lead and zinc.

In the sediment, organic material carries on towards the equilibrium. Moreover, throughout diagenesis proteins and carbohydrates (termed as biogenic polymers or biopolymers) are destroyed via microbial activity. Their constituents become progressively engaged in new polycondensed structures leading to the production of Kerogen. Kerogen is the organic constituent of the sedimentary rocks which is not soluble in the aqueous alkaline solvents or in general organic solvents. The part of sedimentary rock which is soluble in organic solvents is termed as bitumen. Kerogen is the most significant form of organic carbon on earth, and it is 100 times richer as compare coal plus petroleum in reservoirs, and is 50 times richer as compare to bitumen. Kerogens that encompass a high hydrogen/carbon ratio encompass potential for oil and gas generation. Therefore, diagenesis starts in recently deposited sediments where microbial activity takes place. At the end of diagenesis, the organic matter comprises mostly of a fossilized, insoluble organic residue known as Kerogen.


Continuous deposition of sediments yields in the burial of prior bed to a depth reaching some kilometers of overburden in subsiding basins. This leads to a considerable increase in pressure and temperature and. Such increase again places the system out of equilibrium and yields in new changes. There are certain changes in the clay fraction whereas the mineral phase's composition and texture are conserved. The major inorganic modification at this phase comprises the compaction of the rock, water continues to be expelled, porosity and permeability reduces greatly, salinity of the interstitial water increases and might come close to the saturation.

On contrary, liquid petroleum is first generated via the Kerogen produced in the diagenesis phase.  In a later phase, wet gas and condensate are produced. Both the liquid oil and condensate are accompanied by considerable quantity of methane. These are the main changes that the organic matter experience throughout Catagenesis.

The end of Catagenesis is reached whenever the disappearance of aliphatic carbon chain in kerogen is completed.  The Catagenesis yields from an increase in temperature throughout burial in sedimentary basins. Thermal breakdown of Kerogen is accountable for the generation of nearly all hydrocarbons.


The last phase of the evolution of sediments is termed as Metagenesis. It is reached only at great depth, where pressure and temperature are high. At this phase, organic matter is comprised only of methane and a carbon residue. The constituents of residual Kerogen are transformed to graphite carbon. Minerals are severely converted under this condition, clay mineral lose their interlayer water and gain a higher phase of Crystallinity iron oxides having structural water (that is, goethite) change to oxides devoid of water (that is, hematite) and so on severe pressure dissolution and Recrystallisation take place, similar to the formation of quartzite and might result in a disappearance of the original rock structure. The rock reaches temperature conditions which lead to the metagenesis of organic matter. At this phase, the organic matter is comprised only of methane and a carbon residue, where certain crystalline ordering starts to develop. Coals are converted into anthracite.

Transformation of Organic Matter:

The time covering sedimentation methods and residence in the young sediment, freshly deposited, symbolizes a very special phase in the carbon cycle. The first few meters of sediment, just beneath the water-sediment contact, symbolize the interface via which organic carbon passes from the biosphere to the geosphere. The residence period of organic compounds in this zone of the sedimentary column is long compared to the life-time of the organisms, however very short as compared to the time period of geological cycle's example: 1-m section often symbolizes 500 to 10000 years.

Throughout sedimentation processes, and later in such young sediments, organic material is subjected to modifications via varying degrees of microbial and chemical actions. As an outcome, its composition is mostly changed and its future fate throughout the rest of the geological history predetermined in the frame-work of its succeeding temperature history. Whenever comparing the nature of the  organic  material  in young sediments with that of the living organisms from which it was derived, the  striking  point  is  that  most  of  the  general  constituents of such organisms and specifically the  biogenic macromolecules, have disappeared. Proteins, lipids, carbohydrates and lignin in higher plants amount to almost the total dry weight, on an ash-free basis, of the biomass living in the sub-aquatic or sub-aerial atmospheres. The total amount of the similar compounds which can be extracted from very young sediments is generally not more than 20% of the net organic material and often less. This condition results from the degradation of macromolecules by bacteria to individual amino acids, sugars and so on. As monomers, they are employed for nutrition of the microorganisms, and the residue becomes polycondensed, making huge amounts of brown material, partially soluble in the dilute sodium hydroxide and resembling the humic acids.

As an outcome of microbial activity in water and in the sub-aquatic soils, biogenic polymers have been degraded, then employed as much as possible for the metabolism of microorganisms. Therefore, even in fine mud, a portion of the organic matter has been used and has disappeared via transformation into carbon-dioxide and water. The other part has been employed to synthesize the constituents of the microbial cell, and therefore is reintroduced to the biological cycle. The residue which can't be incorporated via microorganisms is now incorporated to a new polycondensate that is an insoluble Kerogen. This chemical method takes place under mild pressure and temperature conditions. Therefore, the affect of the increase of temperature and pressure is probable to be subordinate, compared to the nature of the original organic constituents. This view is verified by the results of experimental evolution tests of heating organic matter under inert atmosphere in order to stimulate the conversions at greater depth that is Catagenesis and Metagenesis however not diagenesis.

At the end of diagenesis, organic matter still includes minor amount of free hydrocarbons and associated compounds. They have been synthesized via living organisms and incorporated in the sediment without or minor modifications. Therefore, they can be considered as geochemical fossils, witnessing the depositional atmosphere. As time and sedimentation carry on, the sediment is buried to some hundreds of meters. Most of the organic material becomes progressively insoluble as an outcome of increasing polycondensation related by the loss of superficial hydrophilic functional groups. This fully insoluble organic matter from sediments has obtained limited attention till recently. It is termed as humin via some soil scientists who have worked on sub-aquatic soils. In ancient sediments, the insoluble organic matter is known as Kerogen and is accomplished by demineralization of the rock. The words humin and Kerogen are not strictly equivalent therefore, humin, collectively by other insoluble organic matter like pollen, spores and so on might be considered as a method of Kerogen. Petroleum geochemists consider Kerogen as the major source of petroleum compounds. The entire process is termed to as diagenesis and leads from biopolymers synthesized via living organisms to geopolymers (Kerogen) via fractionation that is, by separating the mixture into its components, partial destruction and rearrangement of the building blocks of the macromolecules. The conversion of sediments to Kerogen can be supposed to takes place or occur in three that is, biochemical degradation, polycondensation and insolubilisation.

Kerogen is the mixture of organic chemical compounds which make up a part of the organic matter in sedimentary rocks. This is insoluble in normal organic solvents as the huge molecular weight (that is, upwards of 1,000 Daltons) of its component compounds. The soluble part is termed as bitumen. Whenever heated to the right temperatures in the crust of Earth, (that is, oil window ca. 60°-120°C,  gas window  ca. 120°-150°C) some kinds of Kerogen discharge crude oil or natural gas, collectively termed as hydrocarbons (that is, fossil fuels). Whenever such Kerogen is present in high concentration in rocks like shale they form possible source rocks.

Shales  rich  in  Kerogen  which  have  not  been  heated  to  an  adequate temperature to discharge their hydrocarbons might form oil shale deposits. As Kerogen is a mixture of organic material, instead of a particular chemical, it can't be given a chemical formula. Certainly its chemical composition can differ distinctively from sample to sample. Kerogen from the Green River Formation oil shale deposit of western North America includes elements in the proportions C 215 : H 330 : O 12 : N 5 : S 1

There are three kinds of Kerogen namely labile Kerogen, refractory Kerogen and inert Kerogen. Labile Kerogen breaks down to make heavy hydrocarbons (that is, oils), refractory Kerogen breaks down to form light hydrocarbons (that is, gases), and inert Kerogen makes graphite. Though, whenever Van Krevelen diagram is employed (Van Krevelen diagrams are a graphical-statistical process which cross-plots the oxygen: carbon and hydrogen: carbon ratios of petroleum) to categorize kerogen. The given types of Kerogen are arrived at:

Type I:

  • Having alginite, amorphous organic matter, Cyanobacteria, fresh-water algae and land plant resins.
  • Hydrogen: Carbon ratio > 1.25
  • Oxygen: Carbon ratio < 0.15
  • Exhibits great tendency to readily generate liquid hydrocarbons.
  • It derives mainly from lacustrine algae and makes only in the anoxic lakes and some other unusual marine atmospheres.
  • Have some cyclic or aromatic structures
  • Formed mostly from proteins and lipids

1341_Van Krevelan Diagram.jpg

Fig: Van Krevelen Diagram

Type II:  

  • Hydrogen: Carbon ratio < 1.25
  • Oxygen: Carbon ratio 0.03 to 0.18
  • Tend to make a mixture of gas and oil.
  • Some kinds: exinite, cutinite, resinite and liptinite
  • Exinite: made from the casings of pollen and spores
  • Cutinite: made from terrestrial plant cuticle
  • Resinite: formed from terrestrial plant resins and animal decomposition resins
  • Liptinite:  made from terrestrial plant lipids (that is, hydrophobic molecules that are soluble in the organic solvents) and marine algae
  • They all encompass great tendencies to generate petroleum and are all made up from lipids deposited under the reducing conditions.

 Type III

  • Hydrogen: Carbon ratio < 1
  • Oxygen: Carbon ratio 0.03 to 0.3
  • Material is thick, looking like wood or coal.
  • Tends to made coal and gas (recent research has illustrated that type III Kerogen can in reality produce oil under severe conditions).
  • Consists of very low hydrogen due to the extensive ring and aromatic systems

Kerogen Type III is made from terrestrial plant matter which is lacking in lipids or waxy matter.  It prepares from cellulose, the carbohydrate polymer which forms the rigid structure of terrestrial plants, lignin, a non-carbohydrate polymer made up from phenyl-propane units that binds the strings of cellulose altogether, and Terpenes and phenolic compounds in the plant.

Most of the biomass which ultimately becomes petroleum is contributed via the bacteria and protists that decompose the primary matter, not the primary matter itself. Though, the lignin in this Kerogen decomposes to make phenolic compounds which are toxic to bacteria and protists. Without this additional input, it will merely become methane and/or coal.

Type IV (Residue):

Hydrogen: Carbon < 0.5 

Type IV Kerogen includes mostly decomposed organic matter in the form of polycyclic aromatic hydrocarbons. They contain no potential to form hydrocarbons.

From Kerogen to Petroleum:

As the sedimentation and subsidence carry on, temperature and pressure increase. In this changing physical atmosphere, the structure of immature Kerogen is no longer in equilibrium with its surroundings.

Rearrangements will gradually occur to reach a higher, and therefore more stable, degree of ordering.  The steric hindrances for higher ordering have to be removed. They are, for example, non-polar cycles (example: saturated cycles) and linkages with or without heteroatom, preventing the cyclic nuclei from the parallel arrangement.

This constant adjustment of kerogen to increasing temperature and pressure yields in a progressive removal of functional groups and of the linkages between nuclei (comprising carbon chains). A broad range of compounds is formed, comprising medium to low molecular weight hydrocarbons, carbon-dioxide, water, hydrogen sulphide and so on. Thus, the petroleum generation seems to be a necessary consequence of the drive of Kerogen to adjust to its new surroundings via gaining a higher degree of order by increasing overburden.

Kerogen is a polycondensed structure formed beneath the mild pressure and temperature conditions of young sediments and metastable under these conditions. Thus, its features seem to remain instead constant, even in the ancient sediments, as long as they are not buried deeply.  In most of the cases, though, as sedimentation and subsidence proceed, Kerogen is subjected to the progressive increase of pressure and temperature. It is no longer stable under the new condition. Rearrangements take place throughout the successive phases of diagenesis, Catagenesis and Metagenesis toward the thermodynamic equilibrium. 

Diagenesis of Kerogen is marked via decrease of oxygen and a corresponding increase of carbon content by increasing depth. With reference to van Krevelen diagram, this phase of evolution yields in a slight decrease in the ratio of hydrogen/carbon and a marked decrease of   oxygen/carbon.  Infrared spectroscopy has illustrated that the decrease of oxygen is due essentially to the progressive removal of carbonyl (C=O) group. In terms of petroleum exploration, this phase corresponds to an immature Kerogen, and little hydrocarbon generation has occurred in the source rock. Though, large quantities of carbon-dioxide and water and as well some heavy heteroatom (N, S, O) compounds might be generated in relation to the oxygen elimination.

Catagenesis, the second phase of Kerogen degradation, is marked via a significant decrease of the hydrogen content and of the hydrogen to carbon ratio, due to generation and discharge of hydrocarbons. Again, in terms of petroleum exploration, the phase of Catagenesis corresponds to the main zone of oil generation and as well to the starting of the cracking zone that produces 'wet gases by a rapidly increasing proportion of methane. As temperature carries on increasing, the Kerogen reaches the phase of Catagenesis. More bonds of different kinds are broken, such as esters and as well some carbon-carbon bonds, in the Kerogen and within the formerly produced fragments. The new fragments produced become smaller and devoid of oxygen, thus, hydrocarbons are relatively enriched. This corresponds first to the principal stage of oil formation, and then to the phase of 'wet gas' and condensate generation. At similar time, the carbon content rises in the remaining Kerogen, due to the removal of hydrogen. Aliphatic and alicyclic groups are partly eliminated from Kerogen, carbonyl and carboxyl groups are fully removed, and most of the remaining oxygen is comprised in either bonds and possibly in heterocyclic.

Whenever the sediment reaches the deepest portion of the sedimentary basins, temperatures become fairly high. A general cracking of carbon-carbon bond takes place, both in Kerogen and bitumen already produced from it. Aliphatic groups which were still present in Kerogen almost disappear, in the same way, low molecular weight compound, particularly methane, are discharged. The remaining sulphur, if present in Kerogen, is mostly lost, and H2S generation might be significant. This is the principal stage of dry gas formation.

Once most of the labile functional groups and chains are removed, aromatization and polycondensation of the residual Kerogen rises, as illustrated by modification of optical features and by Infra-Red spectra. Parallel arrangement of aromatic nuclei extends over broad areas from 80 to 500Å, making clusters. Physical properties grow accordingly (high reflectance, electron diffraction). This residual Kerogen is not capable to carry on producing hydrocarbons, as illustrated via the negative results of thermo-gravimetric assays. This phase is reached merely in deep or very old sedimentary basins and it corresponds to Metagenesis.

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