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Diagenesis

Diagenesis ( /ˌdaɪəˈdʒɛnɪsɪs/) is the change of sediments or existing sedimentary


rocks into a different sedimentary rock during and after rock formation
(lithification), at temperatures and pressures less than that required for the formation
of metamorphic rocks.[1] It does not include changes from weathering.[1] It is any
chemical, physical, or biological change undergone by a sediment after its initial
deposition, after its lithification. This process excludes surface alteration
(weathering) and metamorphism. These changes happen at relatively low
temperatures and pressures and result in changes to the rock's original mineralogy
A form of diagenesis is
and texture. There is no sharp boundary between diagenesis and metamorphism, but
permineralization, in which buried
the latter occurs at higher temperatures and pressures. Hydrothermal solutions, organisms are replaced by minerals.
meteoric groundwater, porosity, permeability, solubility, and time are all influential These trilobites (Lloydolithus) were
factors. replaced by pyrite during a specific
type of permineralization called
After deposition, sediments are compacted as they are buried beneath successive pyritization.
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 asdissolution 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 andhydrocarbon deposits.

[2]
The process of diagenesis is also important in the decomposition of bone tissue.

Contents
Role of diagenesis in anthropology and paleontology
Role of diagenesis in hydrocarbon generation
Role of diagenesis in bone decomposition
See also
References

Role of diagenesis in anthropology and paleontology


The term diagenesis, literally meaning "across generation",[3] is extensively used in geology. However, this term has filtered into the
field of anthropology, archaeology and paleontology to describe the changes and alterations that take place on skeletal (biological)
material. 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".[4][5] 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).[5]
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.[6] 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.[7] Three general pathways of the diagenesis of bone have been
identified:

1. chemical deterioration of the organic phase.


2. chemical deterioration of the mineral phase.
3. (micro) biological attack of the composite.[8] Originally calcitic crinoid stem (in
cross-section) diagenetically
They are as follows:
replaced by marcasite in a siderite
1. The dissolution of collagen depends on time, temperature and concretion; Lower Carboniferous.
environmental pH.[8] At high temperatures, the rate of collagen loss will
be accelerated and extremepH can cause collagen swelling and
accelerated hydrolysis.[8] Due to the increase inporosity of bones through collagen loss, the bone becomes
susceptible to hydrolyticinfiltration where the hydroxyapatite, with its affinity for amino acids, permits charged
species of endogenous and exogenous origin to take up residence.[2]
2. The hydrolytic activity plays a key role in the mineral phase transformations that exposes the collagen to accelerated
chemical- and bio-degradation.[8] Chemical changes affect crystallinity.[2] Mechanisms of chemical change, such as
the uptake of F− or CO3− may cause recrystallization where hydroxyapatite is dissolved and re-precipitated allowing
[2]
for the incorporation of substitution of exogenous material.
3. Once an individual has beeninterred, microbial attack, the most common mechanism of bone deterioration, occurs
rapidly.[8] During this phase, most bone collagen is lost and porosity is increased. [2] The dissolution of the mineral

phase caused by low pH permits access to the collagen by extracellular microbial enzymes thus microbial attack. [8]

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 ascracking, or catagenesis.

A kinetic model based on experimental data can capture most of the essential transformation in diagenesis,[9] and a mathematical
model in a compacting porous medium to model the dissolution-precipitation mechanism.[10] 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 minerals occurs, the main development of oil
genesis occurs and high to low volatile bituminous coals are formed. During telodiagenesis, organic matter undergoes cracking and
dry gas is produced; semi-anthracite coals develop.[11]

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.[12]

Role of diagenesis in bone decomposition


Diagenesis alters the proportions of organic collagen and inorganic components (hydroxyapatite, calcium, magnesium) of bone
exposed to environmental conditions, especially moisture. This is accomplished by the exchange of natural bone constituents,
[2][13]
deposition in voids or defects, adsorption onto the bone surface and leaching from the bone.

See also
Chalcedony – Microcrystalline varieties of quartz, may contain moganite as well
Chert – A hard, fine-grained sedimentary rock composed of crystals of quartz (silica) that are very small
Flint – Cryptocrystalline form of the mineral quartz
Concretion
Fossil – Preserved remains or traces of organisms from a past geological age

References
1. Marshak, Stephen, 2009,Essentials of Geology, W. W. Norton & Company, 3rd ed. ISBN 978-0393196566
2. Hedges, R. E. M. (2002). "Bone Diagenesis: An Overview of Processes".
Archaeometry. 44 (3): 319–328.
doi:10.1111/1475-4754.00064(https://doi.org/10.1111%2F1475-4754.00064).
3. Oxford English Dictionary.
4. Wilson, L. and M. Pollard, "Here today, gone tomorrow? Integrated experimentation and geochemical modeling in
studies of archaeological diagenetic change".Accounts of Chemical Research, 2002. 35(8): p. 644–651.
5. Zapata, J.; et al. (2006). "Diagenesis, not biogenesis: T
wo late Roman skeletal examples".Science of the Total
Environment. 369 (1–3): 357–368. Bibcode:2006ScTEn.369..357Z(http://adsabs.harvard.edu/abs/2006ScTEn.369..
357Z). doi:10.1016/j.scitotenv.2006.05.021 (https://doi.org/10.1016%2Fj.scitotenv.2006.05.021). PMID 16828844 (htt
ps://www.ncbi.nlm.nih.gov/pubmed/16828844).
6. Nicholson, R. A. (1996). "Bone Degradation, Burial Medium and Species Representation: Debunking the Myths, and
Experiment-based Approach".Journal of Archaeological Science. 23 (4): 513–533. doi:10.1006/jasc.1996.0049(http
s://doi.org/10.1006%2Fjasc.1996.0049).
7. Nielsen-Marsh, C. M. (2000). "Patterns of Diagenesis in Bone I: The Ef
fects of Site Environments".Journal of
Archaeological Science. 27 (12): 1139–1150. doi:10.1006/jasc.1999.0537(https://doi.org/10.1006%2Fjasc.1999.053
7).
8. Collins, M. J.; et al. (2002). "The Survival of Organic Matter in Bone: A Review".Archaeometry. 44 (3): 383–394.
doi:10.1111/1475-4754.t01-1-00071(https://doi.org/10.1111%2F1475-4754.t01-1-00071) .
9. Abercrombie, H. J.; Hutcheon, I. E.; Bloch, J. D.; Caritat, .P(1994). "Silica activity and the smectite-illite reaction".
Geology. 22 (6): 539–542. doi:10.1130/0091-7613(1994)022<0539:saatsi>2.3.co;2(https://doi.org/10.1130%2F0091
-7613%281994%29022%3C0539%3Asaatsi%3E2.3.co%3B2) .
10. Fowler, A. C.; Yang, X. S. (2003). "Dissolution/precipitation mechanisms for diagenesis in
sedimentary basins". J.
Geophys. Res. 108 (B10): 2269. Bibcode:2003JGRB..108.2509F(http://adsabs.harvard.edu/abs/2003JGRB..108.25
09F). CiteSeerX 10.1.1.190.4424 (https://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.190.4424) .
doi:10.1029/2002jb002269(https://doi.org/10.1029%2F2002jb002269).
11. Foscolos, A. E.; Powell, T. G.; Gunther, P. R. (1976). "The use of clay minerals and inorga
nic and organic
geochemical indicators for evaluating the degree of diagenesis and oil generating potential of shales".
Geochimica et
Cosmochimica Acta. 40 (8): 953–966. Bibcode:1976GeCoA..40..953F(http://adsabs.harvard.edu/abs/1976GeCoA..4
0..953F). doi:10.1016/0016-7037(76)90144-7(https://doi.org/10.1016%2F0016-7037%2876%2990144-7) .
12. Lovley, D. R. (1991). "Dissimilatory Fe(II) andMn(IV) reduction". Microbiological Reviews. 55 (2): 259–287.
13. "Beyond the grave: understanding human decomposition" A. A. ass
V Microbiology Today 2001 [1] (http://pathstokno
wledge.files.wordpress.com/2010/07/beyond-the-grave-understanding-human-decomposition-no-photos-v1.pdf)

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