In geology and oceanography, diagenesis is any chemical, physical, or biological change undergone by a sediment after its initial deposition and during and after its lithification, exclusive of surface alteration (weathering) and metamorphism. These changes happen at relatively low temperatures and pressures and result in changes to the rock's original mineralogy and texture. There is no sharp boundary between diagenesis and metamorphism, but the latter occurs at higher temperature and pressure than the former.
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 fossils can be replaced by other minerals during diagenesis. Porosity usually decreases during diagenesis, except in rare cases such as dissolution of minerals and dolomitization.
The study of diagenesis in rocks is used to understand the tectonic history they have undergone; 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.
Lithification (from the Greek word lithos meaning 'rock' and the Latin-derived suffix -ific) is the process in which sediments compact under pressure, expel connate fluids, and gradually become solid rock. Essentially, lithification is a process of porosity destruction through compaction and cementation. Lithification includes all the processes which convert unconsolidated sediments into sedimentary rocks. Petrification, though often used as a synonym, is more specifically used to describe the replacement of organic material by silica in the formation of fossils. In geology consolidation is a synonym for lithification.
The role of diagenesis in anthropology and paleontology
The term diagenesis is extensively used in geology. However, this term has filtered into the field of anthropology and paleontology to describe the changes and alterations that take place on skeletal (biological) material in a burial context. Specifically, diagenesis “is the cumulative physical, chemical and biological environment; these processes will modify an organic object’s original chemical and/or structural properties and will govern its ultimate fate, in terms of preservation or destruction”. In order to assess the potential impact of diagenesis on archaeological or fossil bones, many factors need to be assessed, beginning with elemental and mineralogical composition of bone and enveloping soil, as well as the local burial environment (geology, climatology, groundwater).
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 disintegration of the complete unit. Three general pathways of the diagenesis of bone have been identified:
- chemical deterioration of the organic phase.
- chemical deterioration of the mineral phase.
- (micro) biological attack of the composite.
They are as follows:
- The dissolution of collagen depends on time, temperature and environmental pH. At high temperatures, the rate of collagen loss will be accelerated and extreme pH can cause collagen swelling and accelerated hydrolysis. Due to the increase in porosity of bones through collagen loss, the bone becomes susceptible to hydrolytic infiltration where the hydroxyapatite, with its affinity for amino acids, permits charged species of endogenous and exogenous origin to take up residence.
- The hydrolytic activity plays a key role in the mineral phase transformations that exposes the collagen to accelerated chemical- and bio-degradation. Chemical changes affect crystallinity. Mechanisms of chemical change, such as the uptake of F- or CO3- may cause recrystallization where hydroxyapatite is dissolved and re-precipitated allowing for the incorporation of substitution of exogenous material.
- Once an individual has been interred, microbial attack, the most common mechanism of bone deterioration, occurs rapidly. During this phase, most bone collagen is lost and porosity is increased. The dissolution of the mineral phase caused by low pH permits access to the collagen by extracellular microbial enzymes thus microbial attack.
The role of diagenesis in hydrocarbon generation
When animal or plant matter is buried during sedimentation, the constituent organic molecules (lipids, proteins, carbohydrates and lignin-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: kerogens and bitumens.
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.
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- Geological processes
- Fossil fuels
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