Abiotic: Physical and chemical conditions not directly associated with life forms, but interact with biotic conditions to form ecosystems. For example, salinity, pH, temperature, precipitation. The term includes organic compounds present in abiotic conditions such as comets. Cf. prebiotic.

Acid: A substance that releases or donates a proton when dissolved in water. The proton is a hydrogen ion that in solution associates with an H₂0  molecule to form H₃0⁺ , but is usually written as H⁺ . Acids react with bases (bases contain hydroxyl ions – OH^– ). Water may act as an acid or a base. Solutions with excess H⁺ are acidic, such that pH < 7.

Activity (geochemical): Sometimes referred to as effective concentration. The activity of an ion is the ratio of its concentration versus some standard concentration and is therefore dimensionless (unlike concentration). The ratio is calculated using an activity coefficient. It is used in equilibria because it expresses the amount of an anion or cation that is available for reaction; compare concentration that measures the total amount of an ion. In a solution like sea water there are many different cations and anions, all reacting to collisions of various kinds. For example, the CO₃^2- anion may collide with cations other than Ca²⁺ (Na⁺, Mg²⁺, K⁺ and so on), such that the amount of CO₃^2- available to react with Ca²⁺ is less than the measured concentration. In other words, the amount of CO₃^2- available in real solutions depends not just on its overall concentration, but also on its environment. For this reason, it is preferable to use activities in thermodynamic calculations, such as equilibrium constants. The activity of solids is usually taken as 1.

Activity coefficient:  The activity coefficient (γ) for a specific ion species is related to the degree of ionic interaction with other species in solution. For dilute solutions γ approaches 1 because there are few ion interactions (γ is dimensionless). Thus, the γ value for HCO₃^– in fresh river water averages about 0.95, but in sea water is much lower (0.57) because of ionic interactions. Activity (a) is calculated for specific ions from the relationship:

a = γ m where m is concentration.

 

Aeolianite: Dune sands cemented by calcite are an example of shallow meteoric-vadose zone diagenesis. Dune sand mineralogy may be siliciclastic or bioclastic, or a mix of both. Most common in subtropical to tropical coastal dunes.

Aerobic conditions: Reactions that directly utilise available oxygen, the most obvious being respiration in life forms, where oxygen is used in metabolic reactions to generate energy (e.g., from food). In sediments this generally is associated with the metabolic activity of microbes – a distinction is made between these types of reaction and oxidation reactions that do not require intermediary metabolic activity in life forms. Cf. Anaerobic conditions.

Alizarin Red-S: This is a soluble organic acid that reacts with calcium. Distinguish between calcite (stains pink-red) and dolomite (no stain) can be easily done using this stain, on rock slabs or thin sections.

Alkalinity: Alkalinity is a measure of the amount of acid that can be added to an aqueous solution without causing significant changes to the pH; also referred to as the acid neutralizing capacity or buffering capacity. The total alkalinity of seawater is primarily determined by the major anions:

mHCO₃^– + 2mCO₃^2- + minor constituents like borate, phosphate, and silicate anions.

 

Anaerobic conditions: conditions where metabolic reactions in life forms do not require molecular oxygen. In sediments, such reactions are commonly generated by microbes that reduce oxygen-bearing compounds like sulphate (to sulphide), nitrate (to nitrite or ammonia), and carbon dioxide to methane. Sediment where these conditions persist tend to be green-black, and may have mineral sulphides (e.g., iron, manganese). One example is the sediment beneath wetlands, including marginal marine mangrove wetlands. Cf. aerobic conditions.

Anoxic conditions: Usually applied to aqueous environments (water masses as well as connate water) where there is none, or insufficient dissolved oxygen for respiration; usually measured at less than 0.5 ml/L. Under these conditions, the sources of oxygen via bacterial reduction are from nitrates and sulphates. Once these sources are depleted carbon dioxide becomes an important source during reduction to methane. Deep waters in lakes where there is no turnover of the water mass, can become anoxic. Anoxia are also implicated in some of Earth’s major extinctions, such as the Late Permian – Triassic event. Early Precambrian oceans and lakes were probably anoxic. e.g., März and Brumsack, 2015.

Base: A base is a substance that gains a proton in aqueous solution. This can be written in a generalized way as  H⁺ + OH^– = H₂0.  Water can act as a base or an acid. Solutions with excess OH^– are basic with pH > 7.

Botryoidal cement: In limestones, this cement form is presented as radial clusters of fibrous or bladed calcite or aragonite that precipitate in more cavernous porosity. Common examples are found in reef frameworks, and fenestrae that form by mineral dissolution, gas bubbles, and crystal expansion (e.g. halite-gypsum crystal growth in sabkhas). Fenestrae are common in some cryptalgal laminates and mud mounds containing Stromatactis.

Brines: Generally used for natural waters more saline than seawater. The main dissolved salt is sodium chloride (NaCl), but calcium and magnesium sulphates are also important constituents, and there are several important trace elements, such as lithium. The primary mechanism for brine concentration in ocean basins and saline lakes is evaporation. The saturation level for NaCl is about 357 ppt (normal seawater is 32 ppt).

Calcite compensation depth (CCD): As ocean water depths increase, the partial pressure of CO₂ increases and the temperature decreases – in both cases CaCO₃ becomes increasingly soluble. An important consequence of this convergence is a decrease in CaCO₃ saturation to the point where calcite and aragonite begin to dissolve. For calcite, the depths range from about 4.6 to 5.1 km. Aragonite is more soluble and the ACD depths are about 3 km. This means that the sea floor at or below these depth limits will tend to be devoid of calcareous sediment (particularly microfossils like foraminifera and coccoliths).

Calcite divide (geochemistry):  The stage during evaporation of brines where calcite precipitation determines the succession of minerals in waters subsequently depleted in Ca²⁺ and CO₃^2-. It determines whether the brine subsequently evolves as HCO₃ rich or  HCO₃ poor.

Caliche: Also called calcrete. Soil horizons in which carbonate precipitation results in a hardened crust. They develop in regions in which evaporation exceed precipitation, where periods of wetting alternate with drying. Thus, carbonate textures commonly show evidence of dissolution and reprecipitation. A common product is vadose pisoids that also show evidence of multiple episodes of dissolution and precipitation. They can develop in alluvial-lacustrine and intertidal-supratidal settings.

Capillary zone:  In hydrogeology, also called the capillary fringe.  It is a relatively narrow interval above the watertable where surface tension forces on aquifer materials cause water to rise and partly fill pore spaces. The capillary fringe is part of the unsaturated, or vadose zone.

Carbonates: The most diverse group of sediments and sedimentary rocks, usually presented as limestones and dolostones. Carbonate precipitation (and dissolution) is based on the chemical equilibria involving CO₂, HCO₃^–, CO₃^2-, and H₂CO₃. Their primary mineralogy includes calcite and aragonite polymorphs (CaCO₃), and dolomite (Ca.Mg [CO₃]₂). Carbonate formation at Earth’s surface is intimately associated with biological production where precipitation is either induced directly by organisms, or indirectly promoted by the activity and metabolism of organisms. Organisms involved in carbonate production range from microbial to large invertebrates.

Carbonic acid: A weak acid that forms naturally from the reaction:

CO₂ + H₂O = H₂CO₃

It is the primary cause of slight acidity of rain (pH 5.5 to 5.8). It is an important component in the series of carbonate equilibria, particularly for pH buffering.

Chalcedony: A fibrous form of microcrystalline quartz, or chert. It commonly form radial clusters. Under crossed polars, extinction patterns are sweeping or radial.

Chemical equilibria: Chemical reactions normally written with the reactants on the left and products on the right. The two are separated by either:

• An equal sign indicating equilibrium, where forward reactions (to the right) equal reverse reactions, or
• By two opposing arrows that indicate forward and reverse reactions.

Equilibria should be charge and mass balanced. The quantities of reactants and products are written as concentrations or activities.

Chemical equilibrium: At equilibrium there is no net gain or loss of reactants (by convention, the left side of the equation) or products and no net change in energy. Note that this does not mean the system is static – even at equilibrium there are still collisions between ions (all reactions in solution involve collisions), but collisions on the left equal those on the right side of the equation.

Chemical facies: (hydrogeology) This is a useful concept to demonstrate the chemistry of groundwater in relation to aquifer rock-sediment composition, and the evolution of groundwater chemistry as it flows from one rock type to another. For example, flow from sandstone to limestone aquifers will be accompanied by a change in HCO₃^– and pH, plus the concentrations of cations like calcium and magnesium.

Chemical kinetics: Also called Reaction kinetics. This is the study of reaction rates and reaction pathways, and hence is distinct from thermodynamics that deals with energy transfer during reactions and is independent of rate. Kinetics is a measure of the rate of change (in concentration or activity) of both reactants and products, in reversible and irreversible reactions. It is particularly important in reactions that are slow relative to mass/solute transport. A good example if these conditions is the precipitation of dolomite under surface conditions – the reaction is thermodynamically favoured, but kinetically is very slow. Kinetics is related to thermodynamics in terms of equilibrium constants, the activation energy of reactions (i.e. Gibbs free energy), and temperature. As a general rule, the rate of 1st-order reactions doubles for every 10º increase in temperature.

Chemocline: A boundary within a water column at which there is a fairly abrupt change in chemical gradient. Examples include the boundary between fresh water and seawater, or changes in REDOX conditions, from oxidation to reducing.

Chemotroph: Organisms that obtain their metabolic energy and synthesize biomass (such as carbohydrates) from reduced elements like sulphur, sulphide, and ferrous iron, instead of sunlight.

Chlorite: has low birefringence, in varying shades of green (in PPL), and crystal habit that is also variable, from fibrous, spherulitic or vermiform (worm-like). May be pleochroic in shades of green and yellow. It is commonly associated with low grade metamorphism and hydrothermal alteration. In greywackes and other mud rocks it is a common replacement for clay matrix, micas, and  ferromagnesian minerals.

Clathrate: A general term for gas molecules that become trapped in an ice crystal cage. There are no chemical bonds between the gas and water ice and the gas can be released upon melting. Also called gas hydrates. Vast amounts of methane are trapped this way beneath the sea floor and in permafrost.

Cleavage: A plane of weakness within a crystal that will break with relative ease. It is caused by weak bonds between planes of atoms within a crystal lattice; the pattern of weakness repeats regularly through a crystal. Some minerals have poor or no cleavage (e.g., quartz, olivine); others have excellent cleavage along several lattice planes (e.g., calcite, feldspar). Cleavage is a defining characteristic of a mineral, particularly in thin section.

Compaction:  The process where sediment particles, once deposited, are pushed closer together to form a more tightly knit framework. Compaction begins almost immediately following deposition and continues during sediment burial. The normal compressive stress in this case is applied by the overlying sediment. Because porosity is also reduced, an additional requirement for compaction to take place is the release of interstitial water through aquifers. If fluid cannot escape (for example because of permeability barriers) then the rock body will not compact, and internal fluid pressures will rise – this is called overpressure. Mudrocks can compact to less than a tenth their depositional thickness. More rigid frameworks like sandstones compact far less. See also pressure solution, lithic fragments.

Crystallographic axes: Three or four axes about which a crystal can be rotated through 360^o.  The axes intersect at a single point (the centre of symmetry). They are labelled according to their lengths. If axes are the same length, then they are referred to as a₁, a₂, a₃ etc. If they have different lengths, they are labelled a, b, and c. Thus, in the cubic (isometric) crystal system they are labelled a₁, a₂, a₃, and in the tetragonal system a₁, a₂, c. The hexagonal system is the only one with four axes. Angles between axes are labelled α, β, γ.

Crystal symmetry: Symmetry describes the shape of an object and can be represented both mathematically and visually. In crystallography, the two most useful forms of symmetry are (mainly because they are the easiest to visualize):

1. Axes of rotation (crystallographic axes) where a particular crystal face will be repeated during rotation through 360^o. The number of repetitions for a 360^o rotation can be 2, 3, 4, or 6, that are referred to as two-fold, three-fold, four-fold, and six-fold (axial) symmetry respectively.
2. Planes of symmetry where two parts of a crystal are mirror images. For an analogy, think of this concept in terms of the common bilateral symmetry in many living organisms, such as people, and many classes of mollusc. Note that planes of symmetry are NOT the same as twin planes.
3. Additional elements of symmetry include: A centre of symmetry, where a crystal face is reflected from one side to another or is repeated by inversion, and an axis of rotary inversion.

Crystal systems: There are 6 crystal systems based on combination of the elements of symmetry; a seventh system – trigonal – is usually considered a subclass of the hexagonal system. There are 32 crystal classes based on combinations of the symmetry elements. The defining criteria are axial lengths, the angles between axes, and axial symmetry (the number of repetitions about an axis).

Cubic (or Isometric) crystal system: The most symmetric group. All three axes are the same length and are at right angles to each other.

a₁ = a₂ = a₃                  α = β = γ = 90^o

2, 3, and 4-fold symmetry depending on the class

Common crystal forms: cubes, octahedra, dodecahedra.e.g., Halite, pyrite, fluorite, garnet

Diagenesis:  The sum of physical and chemical processes in sediment, beginning soon after deposition at or immediately below the sediment-water interface, and continuing at depth in concert with increased burial temperatures, lithostatic and hydrostatic pressures, and changing fluid composition.

Dissequilibrium compaction:  Under normal conditions of compaction, fluid that is driven from pore spaces escapes without a significant increase in pore pressure – i.e. hydrostatic conditions prevail.  However, rapid deposition of low permeability deposits can impede fluid flow and under these conditions pore pressures increase; this process is called disequilibrium compaction. In many basins, this occurs at about 3km burial depths. Disequilibrium compaction is enhanced by cementation and tectonic compression.

Dispersion: In geofluids this is the process where dissolved and insoluble compounds move from their source or point of origin; observed in groundwater flow, diagenesis, and metamorphism. In these contexts there are two primary mechanisms – mechanical dispersion, and molecular diffusion.

Drusy cement: Cements consisting of calcite rhomb mosaics that line and fill pores, intraskeletal chambers, and more cavernous porosity. The size of calcite rhombs commonly increases towards the center of void spaces. Intercrystalline boundaries tend to be planar. They are common in meteoric and burial environments where they may overlie earlier fibrous or bladed cements.

Equilibrium constant: For a specific reaction, equilibrium constants are the ratio of product activities (or concentrations) divided by reactant activities; they can be determined experimentally (assuming a reaction is at equilibrium) or using thermodynamic considerations (where activities must be used). The general expression for a reaction involving ionic species in solution is:      aA + bB ↔ cC + dD, where a, b, c, and d are the stoichiometric values for each ion (e.g. 2H⁺).

K = cC + dD/ aA + bB at equilibrium.

In a real aqueous solution, we can determine whether a reaction will proceed to the left or right: if  cC + dD/ aA + bB is <K the reactants will convert to products (the reaction goes to the right. The opposite occurs if cC + dD/ aA + bB >K.

K is strongly dependent on temperature and pressure.

 

Euxinic conditions: Ocean waters that are depleted in dissolved oxygen (anoxic) and are sulphidic. The sulphide is primarily dissolved H₂S. Euxinia can occur in highly stratified water bodies, such as lakes and enclosed seas where there may be an the anoxic layer occurs beneath shallower waters with varying amounts of dissolved oxygen. However, euxinia may also have occurred in larger oceanic water masses in the geological past.

Evaporative pumping:  In arid regions, intense evaporation at the surface creates a hydraulic gradient in shallow subsurface aquifers, inducing lateral groundwater and/or seawater flow to replace lost fluid. Vertical capillary flow through the unsaturated zone (above the watertable) transfers these saline fluids from the aquifer to the surface.

Ferric (iron): Fe³⁺, or Iron III. is the common oxidized state of iron. It is the primary form of iron in limonite (FeO(OH)·nH₂O) and hematite (Fe₂O₃). Magnetite (Fe²⁺ Fe³⁺₂ O₃ contains both iron II and iron 111. The oxidised state produces the red colouration in red beds and red shales.

Ferrous (iron): Fe²⁺, or Iron II. This is the common reduced state of iron in aqueous solution and common minerals like siderite (FeCO₃), iron sulphate (FeSO₄^2-), iron sulphide (FeS), and pyrite (FeS₂). It combines with iron III in magnetite, and substitutes for calcium (Ca²⁺) in ferroan calcite, and for magnesium in ferroan dolomite. Iron II is largely responsible for the greenish hues of reduced shales.

Geothermal gradient: Temperature generally increases with depth in the crust; the gradient for a particular location is stated as the temperature increase per unit depth. The global average is 3^o C/ 100 m although there can be large departures from these values in regions of geothermal and volcanic activity, or regions that have cooled significantly over geological time, such as old oceanic crust.

Goldschmidt classification: The grouping of elements according to their place in the periodic table and their preferred mineral-forming phases. The four main groups are:

• Lithophile elements – those that bond readily with oxygen; tend to concentrate in the crust: Al, At, B, Ba, Be, Br, Ca, Cl, Cr, Cs, F, I, Hf, K, Li, Mg, Na, Nb, O, P, Rb, Sc, Si, Sr, Ta, Th, Ti, U, V, Y, Zr, W, plus the Lanthanides.
• Siderophile elements – iron-loving, mostly avoid oxygen, concentrated in the core and mantle: Au, Co, Fe, Ir, Mn, Mo, Ni, Os, Pd, Pt, Re, Rh, Ru.
• Chalcophile elements – bond with sulphur to form insoluble sulphides – low affinity for oxygen. The elements: Ag, As, Bi, Cd, Cu, Ga, Ge, Hg, In, Pb, Po, S, Sb, Se, Sn, Te, Tl, Zn
• Atmophile elements – H, C, N, noble gases: mostly form gases.

Greenhouse effect: The heating of an atmosphere when gas molecules absorb certain frequencies of solar infrared energy. On Earth this involves water vapour, carbon dioxide, methane, and to a lesser extent nitrous oxide. Molecular oxygen and nitrogen do not absorb infrared energy. Carbon dioxide and water vapour absorb energy at different frequencies. Note that the amount of water vapour in the atmosphere depends on temperature, unlike carbon dioxide.

Groundwater residence time: The time from recharge (usually at the surface) to discharge. Residence times are briefest in unconfined aquifers, ranging from days to years. In regional groundwater flow systems these times are measured in 10⁵ to 10⁶ years. Groundwater dating utilises trace compounds such as fluorocarbons, isotopes like ³H (tritium from atmospheric atomic device testing), and cosmogenic isotopes such as Carbon-14, and Beryllium-10.

Gypsum divide: The stage during evaporation of brines where gypsum precipitation determines the succession of minerals in waters subsequently depleted in Ca²⁺ and SO₄^2-.  It determines whether the brines evolve as SO₄ rich – Ca poor, or SO₄ poor.

Halides: Anions of the Chemical Periodic Table halogen group: Fluoride F‾, chloride Cl‾, bromide Br‾, Iodide I‾, and astatide At‾. Many inorganic halides are water-soluble; most organic halides are not.

Hexagonal crystal system: This system has 4 axes, 3 of which are perpendicular to c axis.

a₁ = a₂ = a₃ ≠ c             Angles between a₁ = a₂ = a₃ = 120^o

6-fold symmetry. Common crystal forms: Prisms, bipyramids. e.g., apatite, beryl. The Trigonal subsystem has one 3-fold axis or rotation. Three important examples are quartz, calcite and dolomite, commonly formed as bipyramids, rhombohedra, and scalenohedra.

Holomict: Lakes or seas in which there is mixing of surface and deeper waters. Bottom waters tend to be oxygenated Cf. Meromict.

Hydrolysis: Also called dissociation. The reversible reaction where H₂0 splits into a hydrogen ion and a hydroxyl ion, as in H₂0 = H⁺ + OH^–. The equilibrium constant is written as:

K_w = (H⁺).(OH^–)/( H₂0). The activity of H₂0 is usually taken as 1.0, so that K_w = (H⁺).(OH^–). At 25ºC K= 10^-14.0 . Where the concentration, or activity of (H⁺) > (OH^–) is acidic, and (H⁺) < (OH^–) is basic. This is the basis for the pH scale, calculated as the -log₁₀  of the activities.

Hypersaline: Having salinity greater than seawater (>35 parts/1000). Modern hypersaline environments are most common between the tropics but are found in such diverse places as the Antarctic dry valleys. Plant and animal life require specialized adaptations to survive these conditions. Prolonged hypersalinity may result in evaporite deposits in lakes and seas.

Karst:  A landscape of gullies, canyons, and steep-sided pinnacles resulting from intense meteoric diagenesis (dissolution) of thick limestones. The relief on karst landforms ranges from 1-2 m to 100s of metres. The corresponding subterranean structures include sinkholes, caverns and underground streams.

Kerogen: Kerogens are complex organic polymers that form during the breakdown of organic matter during the early stages of sediment burial. Three main types are identified depending on the O/C and H/C ratios of the polymer molecules: Type 1 is derived from algal organic matter, Type II from mainly marine micro-organisms, and Type III from plant material. Kerogen itself begins to break down at temperatures around 60^o-80^oC, as part of the organic diagenetic-maturation process. Identification of the kerogen types preserved in hydrocarbon deposits provides a good indication of the original organic matter.

Lithification: The combination of compaction and cementation that produces hard, hammer-ringing rock from loose, uncompacted sediment. Lithification depends on a complex association of physical and chemical processes. Cementation can occur at very shallow depths in the case of carbonates, or at different stages of burial depending on temperature, and rock – fluid chemistry. Compaction begins soon after deposition and continues at depth.

Lithophile elements: One of the Goldschmidt classification groups of elements that readily bond with oxygen. This means they tend to be concentrated in Earth’s crust and probably the crusts of other rocky planets – common examples are Na, Ca, Mg, Si, Al, K. as well as some of the transition metal elements like Fe, Mn. cf. siderophiles.

Lysocline: The ocean water depth where the dissolution of calcite is first observed in sediment. Its identification requires detailed observation of dissolution textures and is somewhat subjective. It lies above the calcite and aragonite compensation depths; the lysocline should, theoretically, be close to the saturation levels for both minerals.

Magnesium calcite: Also called magnesian calcite. In the calcite crystal lattice, magnesium can occupy the position of calcium, up to about 20 mole percent. Two varieties predominate in carbonate sediments and limestones: Low magnesium calcites (LMC) with <4 mole % Mg), and high magnesium calcites (HMC) with 11-19 mole % Mg). HMC commonly recrystallize to LMC during burial diagenesis.

Mechanical dispersion: In geofluids, this occurs when solute molecules are carried from the source by local eddies around grains or through fractures; this kind of tortuosity takes place at a scale much smaller than the en masse advective flow.  Cf. Molecular diffusion.

Meromict: A stratified lake or enclosed sea where the layers do not mix. Bottom water layers may become anoxic as dissolved oxygen is used up by organisms. In saline waters it applies to salt crystals that precipitate within saturated layers and then sink to the bottom.

Meteoric diagenesis (carbonates): Diagenesis of limestone under fresh-water conditions, both in the vadose (unsaturated) zone, and below the watertable. It is largely controlled by the degree of fresh- water seepage and groundwater flow. Vadose zone diagenesis is dominated by dissolution that, if prolonged, produces caverns, sinkholes (dolines), subterranean streams, and spectacular karst landforms. Dissolved calcium carbonate may reprecipitate as cement and fracture-fill in the saturated zone, and as stalactites-stalagmites in caves.

Molecular diffusion: When a solute gradually mixes with solvent molecules; in geofluids this is primarily water. The process does not involve the physical flow of water, but depends on solvent-solute properties such as polarity and charge, and vibration energies. Cf. Mechanical dispersion.

Monoclinic crystal system:  a ≠ b ≠ c                      α = γ = 90^o, β ≠ 90^o

2-fold symmetry.Common crystal forms: Prisms, pinacoids (flattened prisms).e.g., orthoclase, diopside, sphene, staurolite, most amphiboles.

Neomorphism: Defined by R. Folk in 1965 as the transformation between one mineral and itself or a polymorph. In other words, neomorphism is a product of recrystallisation where the bulk composition does not change, only the size and/or shape of crystals. It is common in carbonate lithologies and involves recrystallisation of both framework clasts and cements. As such it tends to cross-cut pre-existing textures and fabrics; relict textures may be preserved. Aggrading neomorphism is common in micrites where crystals increase in size in a more-or-less radial fashion.

Nitrogen cycle: The natural transfer of nitrogen and nitrogen compounds from air to soils, vegetation, water and back to the atmosphere. The natural cycle is complicated by human interventions via fertilizers (nitrates) and industrial nitrogen oxides that saturate soils and leach into shallow groundwater and surface waters. Most of the natural nitrogen fixing is done by microbes.

Nitrogen fixing: This is an important process for plant uptake of nitrogen. Plants do not get their fill of nitrogen from the air, but from soil and plant microbes (fungi, bacteria) that convert molecular nitrogen in air (N2) to water soluble compounds, principally nitrates (NO₃^– ). Plants utilize this soluble form, taking it up via their roots.

Oil generation window: The temperature range 80° – 120°C where hydrocarbon maturation to liquid oil from  sedimentary organic carbon, is most rapid and most productive. At an average geothermal gradient of 30°C/km, the top of the window occurs at depths of about 3 km. Organic matter subjected to temperatures >120°C is prone to gas formation.

Oil migration: Hydrocarbon production in deeply buried sediments, begins in organic-rich sediment, such as oil shale. Once formed (by a series of complex chemical reactions), the oil (and gas) migrate from the shale or mudstone to more porous and permeable rocks such as sandstones and limestones. Migration is driven buoyancy forces and the flow of deep subsurface groundwater. Migration will continue until the oil is trapped (resulting in an oil field). Oil and gas that isn’t trapped will eventually find its way to the surface or sea floor and escape.

Oil seep: Oil, sometimes accompanied by gases like methane, that leak to the surface via fractures or faults, driven of buoyancy forces, or as a part of spring flow.  The hydrocarbons may be sourced from oil-prone porous rock, or from actual subsurface oil pools.

Orthorhombic crystal system:  a ≠ b ≠ c                      α = β = γ = 90^o

2-fold symmetry. Common crystal forms: Prisms, bipyramids.e.g., olivine, cordierite, hypersthene

Oxidation: The process where an atom provides electrons to another atom of a different element; and oxidized element has lost electrons. Oxidation always occurs with reduction (REDOX reactions). An oxidized element (atom) is capable of gaining electrons, in which case it becomes reduced; the initial oxidized element is referred to as a reducing agent. Thus Fe²⁺  is more reduced than Fe³⁺ ; in the mineral pyrite FeS₂  iron is in the 2+ state and sulphur -1 state.

Ozone: When oxygen molecules (O₂) in the stratosphere are bombarded with high energy ultraviolet light (UV) the molecule splits into two oxygen atoms. Each of these atoms in turn reacts with O₂  to produce ozone, or O₃.  Ozone is responsible for absorbing some of the harmful UV radiation that would otherwise reach the surface of the Earth.

Paleothermometer: Geological, paleontological and chemical tools used to determine the temperature conditions and thermal history of ancient environments, and more deep-seated processes associated with sedimentary basins, igneous and metamorphic events. They are components of rocks such as minerals, isotopes, fossils, and fluids that provide us with either a direct measure or proxies of paleotemperatures. Common examples include vitrinite reflectance of coals, fossil colour, radiogenic blocking temperatures, stable isotopes of oxygen and carbon, fission tracks, and fluid inclusions.

Paragenetic sequence: In sedimentary petrology, the sequence of mineral components precipitated (and dissolved) during diagenesis. Sequential changes in mineral composition and/or crystallographic form reflect evolving fluid compositions, fluid flow, burial temperatures, and compaction. It is analogous to cement stratigraphy.

Pendant cement: Stalactite-like cements that accumulate on the low point of grains during gravity drainage of interstitial fluid. They are common in carbonates subjected to vadose zone diagenesis.

pH: Literally the ‘potential of hydrogen’, is a measure of the acidity or alkalinity of an aqueous solution. It is expressed as:

pH = -Log₁₀ (a_H⁺) where a_H⁺ is the activity of H⁺ in solution.

This means that high concentrations of H⁺ have low pH values. The pH range is 0 to 14; a neutral solution has pH = 7. An acidic solution has a pH <7.0; an alkaline solution >7.0. Pure water at 25^oC has a pH of 7; rain a pH of 5.0 to 5.5 (i.e. slightly acidic because of dissolved CO₂), and seawater 7.5 to 8.1. The variations are partly dependent on temperature and its influence on the carbonate equilibria.

pH buffering: Carbonate equilibria do not operate in isolation. If the amount of dissolved CO_2(aq) is increased this does not mean that the amount of H⁺(aq) will increase by the same amount because some of the CO₂ forms H₂CO₃ (aq), some HCO₃^– (aq), and some CO₃^2- (aq), such that the amount of H⁺ added is small. In other words, the cascade of equilibria acts to buffer the system against large changes in pH.

Phase diagram: The graphical representation of different states for a compound, as solid, liquid, or gas. The phase diagram for water is plotted as pressure against temperature; the triple point where all three phases coexist is at 0.01^oC and 608 pascals (0.006 atmospheres). For carbon dioxide the diagram also shows gas, solid and liquid phases, plus a supercritical liquid phase.

Photosynthesis: A process that converts sunlight energy to chemical energy in plants, cyanobacteria, and algae. One of the chemical products is molecular oxygen(O₂), that in plants is formed from carbon dioxide reacting with water in plant cells to produce sugars and oxygen. It is generally understood that most of Earth’s free oxygen was produced during the Precambrian by cyanobacterial stromatolites.

Photic zone: The uppermost layer of the oceans and lakes where light penetrates; the base of the zone is at about 1% of incident sunlight. On average it is about 200 m deep. It is the layer where more than 95% of photosynthesis by marine organisms takes place.

Ppb: Parts per billion

Ppm: The abbreviation for parts per million. For water this equates to 1mg/Litre.

Ppt: The abbreviation for parts per thousand. Also written as ‰.

 

Piper diagram: A matrix of three triangular plots that map the chemical compositions of water. It is based on normalized percentages of major cations (Calcium, magnesium, potassium, and sodium), and carbonate-bicarbonate, sulphate, and chloride anions. It is useful for tracking the source of groundwater flows in aquifers derived from different rock types, and the evolution of chemical speciation.

Pressure solution: The dissolution of rock components (framework clasts and cements) as a result of differential compressive stress. Common products of pressure solution are stylolites. Conditions required for dissolution to take place are:

• Differential compressive stresses develop at intergranular contacts,
• Interstitial fluids must be undersaturated with respect to the mineral phase under stress,
• Dissolved components are transported from the grain contacts to regions of lower compressive stress; this requires efficient fluid movement, and
• The solute reprecipitates some distance from its point of origin.

Reaction kinetics: See Chemical kinetics.

 

Recrystallisation:  In sedimentary rocks this involves the transformation or replacement of a mineral with itself, and usually entails changes in crystal size and shape (but not bulk composition): as in micritic calcite to sparry calcite, or aragonite to its polymorph calcite. The term was originally coined for the process of annealing in metals, which is a dry process. Recrystallisation in sedimentary rocks is always a wet process that involves dissolution of a mineral at grain boundaries, followed by precipitation. It tends to cross-cut original textures, destroying them in the process.

REDOX: Reactions in which oxidizing and reducing agents combine; thus one atom is oxidized and the other reduced simultaneously. For example, in the sour, toxic gas hydrogen sulphide (H₂S), 2 H atoms lose an electron each to the sulphur atom; 2H⁺ S^2-.

Reduction: When an atom gains electrons it becomes reduced. It has electrons to spare and can donate them to the atom of another element that has a deficit of electrons (i.e. it is oxidized). A reduced element that donates electrons is a reducing agent.  Cf. Oxidation, REDOX.

Saline lake brines:  Unlike seawater, terrestrial brines have widely variable compositions, depending on local soil and bedrock compositions, groundwater chemistry, and the degree of evaporitic drawdown. Typical brines contain Na⁺, Ca²⁺, Mg²⁺, Cl^–, SO₄^2-, HCO₃^–, CO₃^2-, and SiO₂, but concentrations are highly variable. pH ranges from highly alkaline to highly acidic. Evaporation pathways produce a succession of different minerals. See also calcite-gypsum divides.

Saturation: Saturation (Ω) is the ratio of the measured ion activity (or concentration) product and the standard solubility product (K_sp) for a mineral. If Ω >1 then the solution is supersaturated with respect to the mineral; if Ω <1 then it is undersaturated and the mineral will dissolve. If Ω = 1 then the mineral is at equilibrium with the solution.

Saturation depth: In ocean chemistry this boundary identifies when seawater becomes unsaturated with respect to calcite (or aragonite). The saturation depth is determined by comparing the measured solubility product of either the activity or concentrations of Ca²⁺ and CO₃^2- in seawater samples, with the equilibrium solubility product at the same temperature and water pressure.

Secondary porosity: Porosity that is created during burial diagenesis by the dissolution of chemically reactive grains such as carbonates and feldspars. Secondary porosity can enhance the overall porosity of a rock, particularly if primary intergranular pore volumes have been occluded by cements. Secondary pores may be larger than those formed during deposition, where entire grains are dissolved. Partial dissolution along twin or cleavage planes in minerals like feldspar, will result in irregular grain boundaries.

Sequestration: Storage of solid, liquid or gas so that it cannot disperse, or escape. Of recent concern is sequestration of carbon in various forms, particularly CO2 and methane. Natural sequestration occurs on rocks (coal, limestones), soils, and permafrost. Artificial sequestration of supercooled CO2 in certain rock formations (such as depleted oil fields) is considered as one means of controlling CO2 emissions.

Sericite: A flaky white mica and common alteration product of feldspar. In thin section it usually presents as fine ragged crystals (rather than the more uniform muscovite flakes), concentrated along feldspar cleavage planes, or distributed across the entire crystal. It has high birefringence and appears to sparkle against the dull background of altered grains and matrix.

Siderophile elements: Literally iron-loving elements, they include the high density transition metals that bond with iron in solid and molten states. They can also bond with sulphur and carbon. As such they tend to concentrate in Earth’s core and to a lesser extent the mantle. They re rare in the crust. Most, except for Fe and Mn have a low affinity for oxygen. The list includes Ag, As, Bi, Cd, Cu, Ga, Ge, Hg, In, Pb, Po, S, Sb, Se, Sn, Te, Tl, Zn – Sulphur is also a volatile element and at Earth’s surface combines with oxygen to form sulphate anions.

Solubility product: Solubility product expresses whether a mineral will dissolve or precipitate in aqueous solutions, at specified temperatures and pressures. For example, aragonite in seawater, the reaction is CaCO_3(solid) ↔ Ca²⁺_(aq) + CO₃^2-_(aq). At equilibrium the solubility product is

K_sp = (aCa²⁺).(a CO₃^2-) / (a CaCO₃ solid)

The activity of the solid calcite is 1, such that the constant at equilibrium becomes:

K_sp = (aCa²⁺).(a CO₃^2-)

(aCa²⁺).(a CO₃^2-) is also called the activity product. In real solutions, if (aCa²⁺).(a CO₃^2-) is >K_sp, then aragonite will precipitate; if <K_sp it will dissolve. See also saturation.

Solute: A chemical compound that has dissolved in a solvent. In geofluids, the solvent is primarily water; common solutes are various chlorides, sulphates, hydroxides, nitrates and phosphates. In all these compounds, the solute will consist of cations and an anions surrounded by water molecules.

Solute transport: The movement or flow of dissolved mass in a fluid, usually water. The primary mechanisms of transport are advective flow and diffusion. Transport is usually accompanied by chemical reactions.

Solvent: A liquid (usually) capable of dissolving and maintaining solutions of solid compounds. Water is the most prominent geofluid solvent. Organic solvents are important for industrial processes.

Stalactite:  Tubes, straws. and threads of calcite that hang from the ceiling in the drip zone of caves. Groundwater, initially undersaturated with respect to calcite can, with sufficient transfer of atmospheric CO₂, become supersaturated, promoting precipitation. Pillars or columns form when stalactites meet stalagmites, their cave-floor counterpart. They are a type of speleothem, a group of cave precipitation structures that includes cave wall linings (drapery), flowstone, and cave pearls. Stalactites and stalagmites can also form from dripping lava.

Stalagmite: Commonly conical shaped mounds of calcite that grow from cave floors as a result of the steady drip of seepage groundwater. They are the cousin of stalactites.

Strong acid: See weak acid.

 

Structure grumeleuse: A term introduced by Lucien Cayeux in 1935, refers to clotted limestone textures where isolated, diffuse patches of micrite are surrounded by coarser neomorphic spar; the overall texture appears clotted. At times it can be difficult to distinguish between this recrystallisation texture and primary peloidal limestones.

Stylolite:  Saw-tooth like, discordant seams that signify pressure solution of rock components (framework clasts and cements). They are most common in carbonates but can form in siliciclastic rocks. They represent differential compressive stresses at grain-to-grain contacts, the dissolution and mass transfer of carbonate by diffusion and fluid flow. Stylolites commonly parallel bedding (from normal compressive stress) but also form oblique to bedding.

Tetragonal crystal system: Liken this group to isometric crystals stretched along the c axis.

a₁ = a₂ ≠ c                    α = β = γ = 90^o            Mostly 2- and 4-fold symmetry. Common crystal forms: Prisms, bipyramids with or without prisms. e.g., zircon, chalcopyrite, rutile

Thermocline: The ocean layer extending from about 200m to 1000m depth where the temperature decreases rapidly. Below the thermocline the water temperature varies little from about 4^o

Triclinic crystal system:  The least symmetric group. a ≠ b ≠ c                      α ≠ β ≠ γ ≠ 90^o

No axes of symmetry!  Common crystal forms: Prisms, bipyramids. e.g., microcline, plagioclase, kyanite

Triple point: On a phase diagram, it is the point in pressure-temperature space where solid, liquid and gas phases of a compound coexist.

Tufa: A natural, surface precipitate of calcium carbonate in alkaline lakes, rivers, springs and geothermal hot pools, promoted by degassing of CO₂ as the waters exit to the surface. Degassing of CO₂ results in an increase in pH, and concomitant increase in the stability of CO₃^2- and HCO₃^– aqueous species and the degree of calcite saturation. It is also possible that microbial activity also promotes precipitation. Tufas tend to be highly porous; they can encase dead critters and vegetation. Travertines are a denser form of surface calcite precipitation. Extensive deposits are typically terraced.

Twinning: A symmetrical intergrowth of two separate crystals of the same mineral, that share the same mineral lattice. In thin section under crossed nicols, each twin segment will go into extinction at different rotations of the microscope stage. There are many kinds of twinning. For example, plagioclase may show albite, carlsbad, or pericline twins individually or as combinations in the same crystal. Important optical properties of twins that help mineral identification include extinction angle (whether straight or inclined), and 2V angles. Note that twin planes are NOT the same as planes of crystal symmetry.

Unit cell: At the atomic scale, the arrangement of atoms that represents the fundamental structure of a mineral in crystal form. The crystals we see consist of a three-dimensional array of stacked unit cells. This means that the overall shape of the crystal mimics its unit cell. The simplest unit cell is a cube; cubes of the same size will stack perfectly. Not all polygonal geometries allow such stacking, for example cells with triangular sides will stack neatly together, but those with 5-sided faces (pentagons) will not. Consideration of the unit cells and their symmetry forms the basis for definition of the 6 (or 7) crystal systems.

Vadose zone:  The portion of an unconfined aquifer above the watertable where pore spaces are air-filled (and approximately at atmospheric pressure). It is synonymous with unsaturated zone.

Vitrinite reflectance: Vitrinite is a component of coal that forms by thermal alteration of plant tissues.  The intensity of reflection from a polished surface of vitrinite samples increases with coal rank. The reflectance is measured and compared with standard values d to determine coal rank.

Weak acid – strong acid: A general classification that depends on how easily an acid donates a proton (H⁺ ) to a water molecule to form H₃O⁺ . A weak acid will partially dissociate (i.e. split into its constituent H⁺ and anion, leaving some of the acid in solution. All the reactions involving carbonate and carbonic acid are weak acid reactions. Strong acids dissociate completely – they donate all their H⁺ . Common examples include hydrochloric acid (HCl) and sulphuric acid (H₂SO₄).