Editing Diagenesis (section)

== Role in hydrocarbon generation ==
When animal or plant matter is buried during sedimentation, the constituent organic [[molecule]]s ([[lipid]]s, [[protein]]s, [[carbohydrate]]s and [[lignin]]-[[Humus|humic]] compounds) break down due to the increase in [[temperature]] and [[pressure]]. This transformation occurs in the first few hundred meters of burial and results in the creation of two primary products: [[kerogen]]s and [[bitumen]]s.

It is generally accepted that hydrocarbons are formed by the thermal alteration of these kerogens (the ''biogenic'' theory). In this way, given certain conditions (which are largely temperature-dependent) kerogens will break down to form hydrocarbons through a chemical process known as [[cracking (chemistry)|cracking]], or [[Catagenesis (geology)|catagenesis]].

A kinetic model based on experimental data can capture most of the essential transformation in diagenesis,<ref>{{cite journal | vauthors = Abercrombie HJ, Hutcheon IE, Bloch JD, Caritat PD | year = 1994 | title = Silica activity and the smectite-illite reaction | journal = Geology | volume = 22 | issue = 6| pages = 539–542 | doi=10.1130/0091-7613(1994)022<0539:saatsi>2.3.co;2| bibcode = 1994Geo....22..539A }}</ref> and a mathematical model in a compacting porous medium to model the dissolution-precipitation mechanism.<ref>{{cite journal | vauthors = Fowler AC, Yang XS | year = 2003 | title = Dissolution/precipitation mechanisms for diagenesis in sedimentary basins | journal = J. Geophys. Res. | volume = 108 | issue = B10| page = 2269 | doi=10.1029/2002jb002269 | bibcode=2003JGRB..108.2509F| citeseerx = 10.1.1.190.4424 }}</ref> These models have been intensively studied and applied in real geological applications.

Diagenesis has been divided, based on hydrocarbon and coal genesis into: ''eodiagenesis'' (early), ''mesodiagenesis'' (middle) and ''telodiagenesis'' (late). During the early or eodiagenesis stage shales lose pore water, little to no hydrocarbons are formed and [[coal]] varies between [[lignite]] and [[sub-bituminous]]. During mesodiagenesis, dehydration of [[clay mineral]]s occurs, the main development of oil genesis occurs and high to low volatile [[bituminous coal]]s are formed. During telodiagenesis, organic matter undergoes cracking and dry gas is produced; semi-[[anthracite]] coals develop.<ref>{{cite journal | vauthors = Foscolos AE, Powell TG, Gunther PR | year = 1976 | title = The use of clay minerals and inorganic and organic geochemical indicators for evaluating the degree of diagenesis and oil generating potential of shales | doi = 10.1016/0016-7037(76)90144-7 | journal = Geochimica et Cosmochimica Acta | volume = 40 | issue = 8| pages = 953–966 | bibcode = 1976GeCoA..40..953F }}</ref>

Early diagenesis in newly formed aquatic sediments is mediated by microorganisms using different electron acceptors as part of their metabolism. Organic matter is mineralized, liberating gaseous [[carbon dioxide]] (CO<sub>2</sub>) in the porewater, which, depending on the conditions, can diffuse into the water column. The various processes of mineralization in this phase are [[nitrification]] and [[denitrification]], [[manganese oxide]] reduction, [[iron hydroxide]] reduction, [[sulfate reduction]], and [[fermentation]].<ref>{{cite journal | vauthors = Lovley DR | title = Dissimilatory Fe(III) and Mn(IV) reduction | journal = Microbiological Reviews | volume = 55 | issue = 2 | pages = 259–87 | date = June 1991 | pmid = 1886521 | doi = 10.1128/MMBR.55.2.259-287.1991 | pmc = 372814 | doi-access = free }}</ref>