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Diagenesis () is the process of physical change and in first caused by water-rock interactions, microbial activity, and compaction after their deposition. Increased pressure and temperature only start to play a role as sediments become buried much deeper in the Earth's crust. In the early stages, the transformation of poorly consolidated sediments into sedimentary rock (lithification) is simply accompanied by a reduction in porosity and water expulsion (clay sediments), while their main mineralogy assemblages remain unaltered. As the rock is carried deeper by further deposition above, its organic content is progressively transformed into and .
The process of diagenesis excludes surface alteration (weathering) and deep metamorphism. There is no sharp boundary between diagenesis and metamorphism, but the latter occurs at higher and . Hydrothermal solutions, meteoric groundwater, rock porosity, permeability, dissolution/precipitation reactions, and time are all influential factors.
After deposition, sediments are compacted as they are buried beneath successive layers of sediment and cemented by minerals that precipitate from solution. Grains of sediment, rock fragments and can be replaced by other minerals (e.g. calcite, siderite, pyrite or marcasite) during diagenesis. Porosity usually decreases during diagenesis, except in rare cases such as solvation of minerals and dolomitization.
The study of diagenesis in rocks is used to understand the geologic history they have undergone and the nature and type of fluids that have circulated through them. From a commercial standpoint, such studies aid in assessing the likelihood of finding various economically viable mineral and hydrocarbon deposits.
The process of diagenesis is also important in the decomposition of bone tissue.
The composite nature of bone, comprising one-third organic (mainly protein collagen) and two thirds mineral (calcium phosphate mostly in the form of hydroxyapatite) renders its diagenesis more complex. Alteration occurs at all scales from molecular loss and substitution, through crystallite reorganization, porosity, and microstructural changes, and in many cases, to the disintegration of the complete unit. Three general pathways of the diagenesis of bone have been identified:
They are as follows:
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, or catagenesis.
A kinetic model based on experimental data can capture most of the essential transformation in diagenesis, and a mathematical model in a compacting porous medium to model the dissolution-precipitation mechanism. 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 occurs, the main development of oil genesis occurs and high to low volatile are formed. During telodiagenesis, organic matter undergoes cracking and dry gas is produced; semi-anthracite coals develop.
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 (CO2) 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.
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