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Diagenesis () is the process that describes physical and chemical changes in
sediments Sediment is a naturally occurring material that is broken down by processes of weathering Weathering is the deterioration of rocks In geology Geology (from the Ancient Greek γῆ, ''gē'' ("earth") and -λoγία, ''-logia'', ( ...
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 350px, Plates in the crust of Earth Earth's crust is a thin shell on the outside of Earth, accounting for less than 1% of Earth's volume. It is the top component of the lithosphere, a division of Earth's layers that includes the Crust (geology), ...
.Marshak, Stephen, 2009, ''Essentials of Geology,'' W. W. Norton & Company, 3rd ed. In the early stages, the transformation of poorly consolidated sediments into
sedimentary rock Sedimentary rocks are types of rock (geology), rock that are formed by the accumulation or deposition of mineral or organic matter, organic particles at Earth#Surface, Earth's surface, followed by cementation (geology), cementation. Sedimentatio ...

sedimentary rock
(
lithification Lithification (from the Ancient Greek Ancient Greek includes the forms of the Greek language used in ancient Greece and the classical antiquity, ancient world from around 1500 BC to 300 BC. It is often roughly divided into the following per ...
) is simply accompanied by a reduction in porosity and water expulsion (
clay Clay is a type of fine-grained natural soil File:Stagnogley.JPG, Surface-water-Gley soil, gley developed in glacial till, Northern Ireland. Soil is a mixture of organic matter, minerals, gases, liquids, and organisms that together support ...

clay
sediments), while their main
mineralogical Mineralogy is a subject of geology Geology (from the Ancient Greek γῆ, ''gē'' ("earth") and -λoγία, ''-logia'', ("study of", "discourse")) is an Earth science concerned with the solid Earth, the rock (geology), rocks of which it is com ...

mineralogical
assemblages remain unaltered. As the rock is carried deeper by further deposition above, its organic content is progressively transformed into
kerogen Kerogen is solid, insoluble organic matter Organic matter, organic material, or natural organic matter refers to the large source of Carbon compounds, carbon-based compounds found within natural and engineered, terrestrial, and aquatic environm ...
s and
bitumen Asphalt, also known as bitumen (, ), is a sticky, black, highly viscous The viscosity of a fluid In physics, a fluid is a substance that continually Deformation (mechanics), deforms (flows) under an applied shear stress, or external ...

bitumen
s. The process of diagenesis excludes surface alteration (
weathering Weathering is the deterioration of rocks In geology Geology (from the Ancient Greek γῆ, ''gē'' ("earth") and -λoγία, ''-logia'', ("study of", "discourse")) is an Earth science concerned with the solid Earth, the rock (geology ...
) and deep
metamorphism Metamorphism is the change of mineral In geology Geology (from the Ancient Greek γῆ, ''gē'' ("earth") and -λoγία, ''-logia'', ("study of", "discourse")) is an Earth science concerned with the solid Earth, the rock (geology), r ...
. There is no sharp boundary between diagenesis and
metamorphism Metamorphism is the change of mineral In geology Geology (from the Ancient Greek γῆ, ''gē'' ("earth") and -λoγία, ''-logia'', ("study of", "discourse")) is an Earth science concerned with the solid Earth, the rock (geology), r ...
, but the latter occurs at higher
temperature Temperature ( ) is a physical quantity that expresses hot and cold. It is the manifestation of thermal energy Thermal radiation in visible light can be seen on this hot metalwork. Thermal energy refers to several distinct physical concept ...

temperature
s and
pressure Pressure (symbol: ''p'' or ''P'') is the force In physics Physics is the natural science that studies matter, its Elementary particle, fundamental constituents, its Motion (physics), motion and behavior through Spacetime, space ...

pressure
s. 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 Solution may refer to: * Solution (chemistry) Image:SaltInWaterSolutionLiquid.jpg, upMaking a saline water solution by dissolving Salt, table salt (sodium chloride, NaCl) in water. The salt is the solute and the water the solvent. In chemistry ...
. Grains of sediment,
rock Rock most often refers to: * Rock (geology) A rock is any naturally occurring solid mass or aggregate of minerals or mineraloid matter. It is categorized by the minerals included, its Chemical compound, chemical composition and the way in w ...
fragments and
fossil A fossil (from Classical Latin Classical Latin is the form of Latin, Latin language recognized as a Literary language, literary standard language, standard by writers of the late Roman Republic and early Roman Empire. It was used from 75 ...

fossil
s can be replaced by other minerals (''e.g.'',
calcite Calcite is a and the most stable of (CaCO3). The , based on , defines value 3 as "calcite". Other polymorphs of calcium carbonate are the minerals and . Aragonite will change to calcite over timescales of days or less at temperatures exceed ...

calcite
,
siderite :''Siderite is also the name of a type of iron meteorite Iron meteorites, also known as siderites, or ferrous meteorites, are a type of meteorites that consist overwhelmingly of an iron–nickel alloy known as meteoric iron that usually consists of ...

siderite
,
pyrite The mineral In geology and mineralogy, a mineral or mineral species is, broadly speaking, a solid chemical compound with a fairly well-defined chemical composition and a specific crystal structure that occurs naturally in pure form.John P. R ...

pyrite
,
marcasite The mineral marcasite, sometimes called “white iron pyrite”, is iron sulfide (FeS2) with orthorhombic crystal structure. It is physically and crystallographically distinct from pyrite The mineral pyrite (), or iron pyrite, also known as fo ...

marcasite
...) during diagenesis.
Porosity Porosity or void fraction is a measure of the void Void may refer to: Science, engineering, and technology * Void (astronomy), the spaces between galaxy filaments that contain no galaxies * Void (composites), a pore that remains unoccupied in a ...
usually decreases during diagenesis, except in rare cases such as
dissolution Dissolution may refer to: Arts and entertainment Books * Dissolution (Forgotten Realms novel), ''Dissolution'' (''Forgotten Realms'' novel), a 2002 fantasy novel by Richard Lee Byers * Dissolution (Sansom novel), ''Dissolution'' (Sansom novel), a 2 ...

dissolution
of minerals and
dolomitization Dolomitization is a geological process by which the carbonate In chemistry, a carbonate is a salt Salt is a mineral composed primarily of sodium chloride (NaCl), a chemical compound belonging to the larger class of Salt (chemistry), salt ...
. 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 In , a hydrocarbon is an consisting entirely of and . Hydrocarbons are examples of s. Hydrocarbons are generally colourless and hydrophobic with only weak odours. Because of their diverse molecular structures, it is difficult to generalize furth ...
deposits. The process of diagenesis is also important in the decomposition of bone tissue.


Role in anthropology and paleontology

The term diagenesis, literally meaning "across generation",Oxford English Dictionary. is extensively used in
geology Geology (from the γῆ, ''gē'' ("earth") and -λoγία, ''-logia'', ("study of", "discourse")) is a branch of concerned with both the liquid and , the of which it is composed, and the processes by which they change over time. Geology can ...

geology
. However, this term has filtered into the field of
anthropology Anthropology is the of ity, concerned with , , , and , in both the present and past, including . studies patterns of behaviour, while studies cultural meaning, including norms and values. studies how language influences social life. studi ...
,
archaeology Archaeology or archeology is the study of human activity through the recovery and analysis of material culture. Archaeology is often considered a branch of socio-cultural anthropology, but archaeologists also draw from biological, geological ...
and
paleontology Paleontology (), also spelled palaeontology or palæontology, is the scientific study of life that existed prior to, and sometimes including, the start of the Holocene epoch (geology), epoch (roughly 11,700 years before present). It includes th ...
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". In order to assess the potential impact of diagenesis on
archaeological Archaeology or archeology is the study of human activity through the recovery and analysis Analysis is the process of breaking a complexity, complex topic or Substance theory, substance into smaller parts in order to gain a better underst ...

archaeological
or
fossil A fossil (from Classical Latin Classical Latin is the form of Latin, Latin language recognized as a Literary language, literary standard language, standard by writers of the late Roman Republic and early Roman Empire. It was used from 75 ...

fossil
bone A bone is a rigid tissue Tissue may refer to: Biology * Tissue (biology), an ensemble of similar cells that together carry out a specific function * ''Triphosa haesitata'', a species of geometer moth found in North America * ''Triphosa dubit ...

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,
climatology Climatology (from Greek#REDIRECT Greek Greek may refer to: Greece Anything of, from, or related to Greece Greece ( el, Ελλάδα, , ), officially the Hellenic Republic, is a country located in Southeast Europe. Its population is appr ...
,
groundwater Groundwater is the water Water (chemical formula H2O) is an inorganic, transparent, tasteless, odorless, and nearly colorless chemical substance, which is the main constituent of Earth's hydrosphere and the fluids of all known living ...

groundwater
). The composite nature of bone, comprising one-third organic (mainly
protein Proteins are large s and s that comprise one or more long chains of . Proteins perform a vast array of functions within organisms, including , , , providing and , and from one location to another. Proteins differ from one another primarily ...

protein
collagen Collagen () is the main structural in the found in the body's various s. As the main component of connective tissue, it is the most abundant protein in mammals, making up from 25% to 35% of the whole-body protein content. Collagen consists of ...

collagen
) and two thirds mineral (
calcium phosphate Calcium phosphate is a family of materials and mineral In geology Geology (from the Ancient Greek γῆ, ''gē'' ("earth") and -λoγία, ''-logia'', ("study of", "discourse")) is an Earth science concerned with the solid Earth, the rock ...
mostly in the form of
hydroxyapatite Hydroxyapatite, also called hydroxylapatite (HA), is a naturally occurring mineral In geology and mineralogy, a mineral or mineral species is, broadly speaking, a solid chemical compound with a fairly well-defined chemical composition and a ...
) 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 Dissolution may refer to: Arts and entertainment Books * Dissolution (Forgotten Realms novel), ''Dissolution'' (''Forgotten Realms'' novel), a 2002 fantasy novel by Richard Lee Byers * Dissolution (Sansom novel), ''Dissolution'' (Sansom novel), a 2 ...
of collagen depends on time, temperature and environmental pH. At high temperatures, the rate of collagen loss will be accelerated and extreme can cause collagen swelling and accelerated
hydrolysis Hydrolysis (; ) is any chemical reaction in which a molecule of water breaks one or more chemical bonds. The term is used broadly for substitution Substitution may refer to: Arts and media *Chord substitution, in music, swapping one chord for ...

hydrolysis
. Due to the increase in
porosity Porosity or void fraction is a measure of the void Void may refer to: Science, engineering, and technology * Void (astronomy), the spaces between galaxy filaments that contain no galaxies * Void (composites), a pore that remains unoccupied in a ...
of bones through collagen loss, the bone becomes susceptible to hydrolytic
infiltration Infiltration may refer to: Science, medicine, and engineering *Infiltration (hydrology), downward movement of water into soil *Infiltration (HVAC), a heating, ventilation, and air conditioning term for air leakage into buildings *Infiltration (med ...
where the hydroxyapatite, with its affinity for
amino acids Amino acids are organic compounds that contain amino (–NH2) and Carboxylic acid, carboxyl (–COOH) functional groups, along with a Substituent, side chain (R group) specific to each amino acid. The key Chemical element, elements of an amino ...

amino acids
, permits charged species of
endogenous Endogenous substances and processes are those that originate from within a system such as an organism, Tissue (biology), tissue, or Cell (biology), cell. Endogenous substances and processes contrast with exogenous ones, such as Drug, drugs, which ...
and
exogenous In a variety of contexts, exogeny or exogeneity () is the fact of an action or object originating externally. It contrasts with endogeneity or endogeny, the fact of being influenced within a system. Economics In an economic An economy (; ) ...
origin to take up residence. # The
hydrolytic Hydrolysis (; ) is any chemical reaction in which a molecule of water breaks one or more chemical bonds. The term is used broadly for substitution, elimination, and solvation Solvation (or dissolution) describes the interaction of solvent ...
activity plays a key role in the mineral phase transformations that exposes the collagen to accelerated chemical- and bio-degradation. Chemical changes affect
crystallinity Crystallinity refers to the degree of structural order in a solid Solid is one of the four fundamental states of matter (the others being liquid, gas and plasma). The molecules in a solid are closely packed together and contain the le ...
. Mechanisms of chemical change, such as the uptake of F or CO3 may cause recrystallization where hydroxyapatite is dissolved and re-
precipitated Precipitation is the process of conversion of a chemical substance into a solid from a solution by converting the substance into an insoluble form or a Supersaturated solution, super-saturated solution. When the reaction occurs in a liquid solu ...
allowing for the incorporation or substitution of exogenous material. # Once an individual has been
interred Burial, also known as interment or inhumation, is a method of final disposition wherein a dead person or non-human animal is placed into the ground, sometimes with objects. This is usually accomplished by excavating a pit or trench, placing th ...
, 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 permits access to the collagen by extracellular microbial enzymes thus microbial attack.


Role in hydrocarbon generation

When animal or plant matter is buried during sedimentation, the constituent organic
molecule A molecule is an electrically Electricity is the set of physical phenomena associated with the presence and motion Image:Leaving Yongsan Station.jpg, 300px, Motion involves a change in position In physics, motion is the phenomenon ...

molecule
s (
lipid In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanis ...
s,
protein Proteins are large s and s that comprise one or more long chains of . Proteins perform a vast array of functions within organisms, including , , , providing and , and from one location to another. Proteins differ from one another primarily ...

protein
s,
carbohydrate A carbohydrate () is a biomolecule , showing alpha helices, represented by ribbons. This poten was the first to have its suckture solved by X-ray crystallography by Max Perutz and Sir John Cowdery Kendrew in 1958, for which they received a ...
s and
lignin Lignin is a class of complex organic polymers that form key structural materials in the support tissues of most plants. Lignins are particularly important in the formation of cell walls, especially in wood and Bark (botany), bark, because they l ...

lignin
-
humic Humic substances are organic compound In chemistry Chemistry is the study of the properties and behavior of . It is a that covers the that make up matter to the composed of s, s and s: their composition, structure, properties, behavio ...

humic
compounds) break down due to the increase in
temperature Temperature ( ) is a physical quantity that expresses hot and cold. It is the manifestation of thermal energy Thermal radiation in visible light can be seen on this hot metalwork. Thermal energy refers to several distinct physical concept ...

temperature
and
pressure Pressure (symbol: ''p'' or ''P'') is the force In physics Physics is the natural science that studies matter, its Elementary particle, fundamental constituents, its Motion (physics), motion and behavior through Spacetime, space ...

pressure
. This transformation occurs in the first few hundred meters of burial and results in the creation of two primary products:
kerogen Kerogen is solid, insoluble organic matter Organic matter, organic material, or natural organic matter refers to the large source of Carbon compounds, carbon-based compounds found within natural and engineered, terrestrial, and aquatic environm ...
s and
bitumen Asphalt, also known as bitumen (, ), is a sticky, black, highly viscous The viscosity of a fluid In physics, a fluid is a substance that continually Deformation (mechanics), deforms (flows) under an applied shear stress, or external ...

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, 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 Coal is a combustible , Germany ) , image_map = , map_caption = , map_width = 250px , capital = Berlin , coordinates = , largest_city = capital , languages_type = Official language , languages = German language, German , ...

coal
varies between
lignite Lignite, often referred to as brown coal, is a soft, brown, combustible , Germany ) , image_map = , map_caption = , map_width = 250px , capital = Berlin , coordinates = , largest_city = capital , languages_type = Official langu ...

lignite
and sub-bituminous. During mesodiagenesis, dehydration of
clay mineral Clay minerals are hydrous In chemistry, a hydrate is a substance that contains water or its constituent elements. The chemical state of the water varies widely between different classes of hydrates, some of which were so labeled before their ch ...
s occurs, the main development of oil genesis occurs and high to low volatile
bituminous coal Bituminous coal or black coal is a relatively soft coal containing a tarlike substance called bitumen or asphalt. It is of higher quality than lignite and Sub-bituminous coal, Sub-bituminous coal, but of poorer quality than anthracite. Formation ...

bituminous coal
s are formed. During telodiagenesis, organic matter undergoes cracking and dry gas is produced; semi-
anthracite Anthracite, also known as hard coal, is a hard, compact variety of coal that has a lustre (mineralogy)#Submetallic lustre, submetallic luster. It has the highest carbon content, the fewest impurities, and the highest energy density of all types of ...

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 Carbon dioxide (chemical formula A chemical formula is a way of presenting information about the chemical proportions of s that constitute a particular or molecule, using symbols, numbers, and sometimes also other symbols, such as pare ...

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 '' Nitrification'' is the biological oxidation (mild reducing agent) are added to powdered potassium permanganate Potassium permanganate is an inorganic compound with the chemical formula KMnO4 and composed of potassium ion, K+ and permangan ...
and
denitrification Denitrification is a microbially facilitated process where nitrate (NO3−) is reduced and ultimately produces molecular nitrogen Nitrogen is the chemical element upright=1.0, 500px, The chemical elements ordered by link=Periodic tab ...
,
manganese Manganese is a chemical element In chemistry, an element is a pure Chemical substance, substance consisting only of atoms that all have the same numbers of protons in their atomic nucleus, nuclei. Unlike chemical compounds, chemical e ...

manganese
oxide reduction,
iron Iron () is a chemical element In chemistry Chemistry is the study of the properties and behavior of . It is a that covers the that make up matter to the composed of s, s and s: their composition, structure, properties, behav ...

iron
hydroxide reduction, sulfate reduction, and
fermentation Fermentation is a metabolic Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life Life is a characteristic that distinguishes physical entities that have biological processes, such as Cell signalin ...

fermentation
.


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.


See also

* * * * *


References

{{Authority control Geological processes Fossil fuels Sedimentology