View source for Earth:Diagenesis

{{short description|Physico-chemical changes in sediments occurring after their deposition}}
[[File:Pyritized Lloydolithus lloydi.JPG|thumb|upright=1.35|A form of diagenesis is [[Earth:Permineralization|permineralization]], in which buried organisms are replaced by minerals. These trilobites (''Lloydolithus'') were replaced by pyrite during a specific type of permineralization called pyritization.]]
[[File:Permineralization in vertebra from Valgipes bucklandi.tif|thumb|upright=1.35|Permineralization in vertebra from ''[[Biology:Valgipes|Valgipes bucklandi]]'']]

'''Diagenesis''' ({{IPAc-en|ˌ|d|aɪ|.|ə|ˈ|dʒ|ɛ|n|ə|s|ɪ|s}}) is the process that describes [[Physics:Physical change|physical]] and [[Chemistry:Chemical change|chemical change]]s in [[Earth:Sediment|sediment]]s first caused by water-rock interactions, microbial activity, and compaction after their [[Earth:Deposition (geology)|deposition]]. Increased pressure and temperature only start to play a role as sediments become buried much deeper in the [[Earth:Earth's crust|Earth's crust]].<ref Name=EG>{{cite book |last=Marshak|first=Stephen |year=2009 |title=Essentials of Geology |publisher=W. W. Norton & Company |edition=3rd |isbn=978-0393196566}}</ref> In the early stages, the transformation of poorly consolidated sediments into [[Earth:Sedimentary rock|sedimentary rock]] ([[Earth:Lithification|lithification]]) is simply accompanied by a reduction in porosity and water expulsion ([[Earth:Clay|clay]] sediments), while their main [[Earth:Mineralogy|mineralogical]] assemblages remain unaltered. As the rock is carried deeper by further deposition above, its organic content is progressively transformed into [[Earth:Kerogen|kerogen]]s and [[Chemistry:Bitumen|bitumen]]s. 

The process of diagenesis excludes surface alteration ([[Earth:Weathering|weathering]]) and deep [[Earth:Metamorphism|metamorphism]]. There is no sharp boundary between diagenesis and [[Earth:Metamorphism|metamorphism]], but the latter occurs at higher [[Physics:Temperature|temperature]]s and [[Physics:Pressure|pressure]]s. Hydrothermal solutions, meteoric groundwater, rock porosity, [[Earth:Permeability (Earth sciences)|permeability]], dissolution/[[Chemistry:Precipitation|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 [[Chemistry:Solution|solution]]. Grains of sediment, [[Earth:Rock (geology)|rock]] fragments and [[Biology:Fossil|fossil]]s can be replaced by other minerals (e.g. [[Chemistry:Calcite|calcite]], [[Chemistry:Siderite|siderite]], [[Chemistry:Pyrite|pyrite]] or [[Chemistry:Marcasite|marcasite]]) during diagenesis. [[Earth:Porosity|Porosity]] usually decreases during diagenesis, except in rare cases such as [[Chemistry:Solvation|dissolution]] of minerals and [[Earth:Dolomitization|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 [[Chemistry:Hydrocarbon|hydrocarbon]] deposits.

The process of diagenesis is also important in the decomposition of bone tissue.<ref name="Hedges">{{cite journal |last=Hedges|first=R. E. |year=2002 |title=Bone Diagenesis: An Overview of Processes |journal=Archaeometry |volume=44 |issue=3 |pages=319–28 |doi=10.1111/1475-4754.00064|doi-access=free }}</ref>

== Role in anthropology and paleontology ==
[[File:Crinoid stem replaced with marcasite.JPG|thumb|Originally [[Chemistry:Calcite|calcitic]] crinoid stem (in cross-section) diagenetically replaced by marcasite in a siderite concretion; Lower Carboniferous.]]
The term diagenesis, literally meaning "across generation",<ref name="O.E.D.">Oxford English Dictionary.</ref> is extensively used in [[Earth:Geology|geology]]. However, this term has filtered into the field of [[Social:Anthropology|anthropology]], [[Earth:Archaeology|archaeology]] and [[Biology:Paleontology|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".<ref name = "Wilson">{{cite journal|doi=10.1021/ar000203s|pmid=12186569|s2cid=20545137|title=Here Today, Gone Tomorrow? Integrated Experimentation and Geochemical Modeling in Studies of Archaeological Diagenetic Change|year=2002|last1=Wilson|first1=Lyn|last2=Pollard|first2=A. Mark|journal=Accounts of Chemical Research|volume=35|issue=8|pages=644–651}}</ref><ref name = "Zapata">{{cite journal | vauthors = Zapata J, Pérez-Sirvent C, Martínez-Sánchez MJ, Tovar P | title = Diagenesis, not biogenesis: Two late Roman skeletal examples | journal = The Science of the Total Environment | volume = 369 | issue = 1–3 | pages = 357–68 | date = October 2006 | pmid = 16828844 | doi = 10.1016/j.scitotenv.2006.05.021 | bibcode = 2006ScTEn.369..357Z }}</ref> In order to assess the potential impact of diagenesis on archaeological or [[Biology:Fossil|fossil]] [[Biology:Bone|bone]]s, 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, [[Earth:Climatology|climatology]], [[Earth:Groundwater|groundwater]]).<ref name = "Zapata"/>

The composite nature of bone, comprising one-third organic (mainly [[Biology:Protein|protein]] [[Biology:Collagen|collagen]]) and two thirds mineral ([[Chemistry:Calcium phosphate|calcium phosphate]] mostly in the form of [[Chemistry:Hydroxyapatite|hydroxyapatite]]) renders its diagenesis more complex.<ref name="Nicholson">{{cite journal | vauthors = Nicholson RA | year = 1996 | title = Bone Degradation, Burial Medium and Species Representation: Debunking the Myths, and Experiment-based Approach | journal = Journal of Archaeological Science | volume = 23 | issue = 4| pages = 513–533 | doi=10.1006/jasc.1996.0049}}</ref> 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.<ref name = "Neilsen-Marsh">{{cite journal | vauthors = Nielsen-Marsh CM | title = Patterns of Diagenesis in Bone I: The Effects of Site Environments | doi = 10.1006/jasc.1999.0537| journal = Journal of Archaeological Science | year = 2000 | volume = 27| issue = 12 | pages = 1139–1150 }}</ref> 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.<ref name = "Collins">{{cite journal | vauthors = Collins MJ, Nielsen, Marsh CM, Hiller J, Smith CI, Roberts JP, Prigodich RV, Wess TJ, Csapo J, Millard AR | display-authors = 6 | year = 2002 | title = The Survival of Organic Matter in Bone: A Review | journal = Archaeometry | volume = 44 | issue = 3| pages = 383–394 | doi=10.1111/1475-4754.t01-1-00071| doi-access = free }}</ref>

They are as follows:
# The dissolution of collagen depends on time, temperature, and environmental [[Chemistry:PH|pH]].<ref name = "Collins"/> At high temperatures, the rate of [[Biology:Collagen loss|collagen loss]] will be accelerated, and extreme pH can cause collagen swelling and accelerated [[Chemistry:Hydrolysis|hydrolysis]].<ref name = "Collins"/> Due to the increase in porosity of bones through collagen loss, the bone becomes susceptible to hydrolytic [[Earth:Infiltration (hydrology)|infiltration]] where the hydroxyapatite, with its affinity for amino acids, permits charged species of endogenous and exogenous origin to take up residence.<ref name = "Hedges"/>
# The hydrolytic activity plays a key role in the mineral phase transformations that expose the collagen to accelerated chemical- and bio-degradation.<ref name = "Collins"/> Chemical changes affect [[Physics:Crystallinity|crystallinity]].<ref name = "Hedges"/><ref name=":0">{{cite journal | vauthors = de Sousa DV, Eltink E, Oliveira RA, Félix JF, Guimarães LM | title = Diagenetic processes in Quaternary fossil bones from tropical limestone caves | journal = Scientific Reports | volume = 10 | issue = 1 | pages = 21425 | date = December 2020 | pmid = 33293631 | pmc = 7722736 | doi = 10.1038/s41598-020-78482-0 | bibcode = 2020NatSR..1021425D | url = }}</ref> Mechanisms of chemical change, such as the uptake of F<sup>−</sup> or {{chem|CO|3|2-}} may cause [[Chemistry:Recrystallization|recrystallization]] where hydroxyapatite is dissolved and re-precipitated allowing for the incorporation or substitution of exogenous material.<ref name = "Hedges"/><ref name=":0" />
# Once an individual has been interred, microbial attack, the most common mechanism of bone deterioration, occurs rapidly.<ref name = "Collins"/> During this phase, most bone collagen is lost and porosity is increased.<ref name = "Hedges"/> The dissolution of the mineral phase caused by low pH permits access to the collagen by extracellular microbial enzymes thus microbial attack.<ref name = "Collins"/>

== Role in hydrocarbon generation ==
When animal or plant matter is buried during sedimentation, the constituent organic [[Physics:Molecule|molecule]]s ([[Chemistry:Lipid|lipid]]s, [[Biology:Protein|protein]]s, [[Chemistry:Carbohydrate|carbohydrate]]s and [[Biology:Lignin|lignin]]-humic compounds) break down due to the increase in [[Physics:Temperature|temperature]] and [[Physics:Pressure|pressure]]. This transformation occurs in the first few hundred meters of burial and results in the creation of two primary products: [[Earth:Kerogen|kerogen]]s and [[Chemistry:Bitumen|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 [[Chemistry:Cracking|cracking]], or 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 [[Earth:Coal|coal]] varies between [[Chemistry:Lignite|lignite]] and sub-bituminous. During mesodiagenesis, dehydration of [[Chemistry:Clay mineral|clay mineral]]s occurs, the main development of oil genesis occurs and high to low volatile [[Earth:Bituminous coal|bituminous coal]]s are formed. During telodiagenesis, organic matter undergoes cracking and dry gas is produced; semi-[[Chemistry:Anthracite|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 [[Chemistry:Carbon dioxide|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 [[Biology:Nitrification|nitrification]] and [[Biology:Denitrification|denitrification]], [[Chemistry:Manganese oxide|manganese oxide]] reduction, iron hydroxide reduction, sulfate reduction, and [[Biology:Fermentation|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>

== Role 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, deposition in voids or defects, adsorption onto the bone surface and leaching from the bone.<ref name="Hedges"/><ref>{{cite journal|title=Beyond the grave: understanding human decomposition|first= A. A. |last=Vass |journal=Microbiology Today|year= 2001| url=http://www.academia.dk/BiologiskAntropologi/Tafonomi/PDF/ArpadVass_2001.pdf|volume=28}}</ref>

== See also ==
* {{annotated link|Chemistry:Chalcedony}}
* {{annotated link|Earth:Chert}}
* {{annotated link|Earth:Flint}}
* {{annotated link|Earth:Concretion}}
* {{annotated link|Biology:Fossil}}
* {{annotated link|Earth:Petrogenesis}}

== References ==
{{Reflist}}

{{Geologic Principles}}


[[Category:Geological processes]]
[[Category:Sedimentology]]

{{Sourceattribution|Diagenesis}}