Soil liquefaction

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Soil_liquefaction 

Some effects of soil liquefaction after the 1964 Niigata earthquake

Soil liquefaction allowed this sewer manhole to float upward and breach the pavement during the 2004 Chūetsu earthquake

Soil liquefaction in Christchurch. The 2011 earthquake caused a layer of water and fine sand to collect on the surface of this street.

Soil liquefaction occurs when a cohesionless saturated or partially saturated soil substantially loses strength and stiffness in response to an applied stress such as shaking during an earthquake or other sudden change in stress condition, in which material that is ordinarily a solid behaves like a liquid. In soil mechanics, the term "liquefied" was first used by Allen Hazen in reference to the 1918 failure of the Calaveras Dam in California. He described the mechanism of flow liquefaction of the embankment dam as:

If the pressure of the water in the pores is great enough to carry all the load, it will have the effect of holding the particles apart and of producing a condition that is practically equivalent to that of quicksand... the initial movement of some part of the material might result in accumulating pressure, first on one point, and then on another, successively, as the early points of concentration were liquefied.

The phenomenon is most often observed in saturated, loose (low density or uncompacted), sandy soils. This is because a loose sand has a tendency to compress when a load is applied. Dense sands, by contrast, tend to expand in volume or 'dilate'. If the soil is saturated by water, a condition that often exists when the soil is below the water table or sea level, then water fills the gaps between soil grains ('pore spaces'). In response to soil compressing, the pore water pressure increases and the water attempts to flow out from the soil to zones of low pressure (usually upward towards the ground surface). However, if the loading is rapidly applied and large enough, or is repeated many times (e.g., earthquake shaking, storm wave loading) such that the water does not flow out before the next cycle of load is applied, the water pressures may build to the extent that it exceeds the force (contact stresses) between the grains of soil that keep them in contact. These contacts between grains are the means by which the weight from buildings and overlying soil layers is transferred from the ground surface to layers of soil or rock at greater depths. This loss of soil structure causes it to lose its strength (the ability to transfer shear stress), and it may be observed to flow like a liquid (hence 'liquefaction').

Although the effects of soil liquefaction have been long understood, engineers took more notice after the 1964 Alaska earthquake and 1964 Niigata earthquake. It was a major cause of the destruction produced in San Francisco's Marina District during the 1989 Loma Prieta earthquake, and in the Port of Kobe during the 1995 Great Hanshin earthquake. More recently soil liquefaction was largely responsible for extensive damage to residential properties in the eastern suburbs and satellite townships of Christchurch during the 2010 Canterbury earthquake and more extensively again following the Christchurch earthquakes that followed in early and mid-2011. On 28 September 2018, an earthquake of 7.5 magnitude hit the Central Sulawesi province of Indonesia. Resulting soil liquefaction buried the suburb of Balaroa and Petobo village 3 metres (9.8 ft) deep in mud. The government of Indonesia is considering designating the two neighborhoods of Balaroa and Petobo, that have been totally buried under mud, as mass graves.

The building codes in many countries require engineers to consider the effects of soil liquefaction in the design of new buildings and infrastructure such as bridges, embankment dams and retaining structures.

Technical definitions

The Giddy House in Port Royal, Jamaica, which partially sank into the ground during an earthquake in 1907 which produced soil liquefaction, resulting in its distinctive tilted appearance.

Soil liquefaction occurs when the effective stress (shear strength) of soil is reduced to essentially zero. This may be initiated by either monotonic loading (i.e., a single, sudden occurrence of a change in stress – examples include an increase in load on an embankment or sudden loss of toe support) or cyclic loading (i.e., repeated changes in stress condition – examples include wave loading or earthquake shaking). In both cases a soil in a saturated loose state, and one which may generate significant pore water pressure on a change in load are the most likely to liquefy. This is because loose soil has the tendency to compress when sheared, generating large excess porewater pressure as load is transferred from the soil skeleton to adjacent pore water during undrained loading. As pore water pressure rises, a progressive loss of strength of the soil occurs as effective stress is reduced. Liquefaction is more likely to occur in sandy or non-plastic silty soils but may in rare cases occur in gravels and clays (see quick clay).

A 'flow failure' may initiate if the strength of the soil is reduced below the stresses required to maintain the equilibrium of a slope or footing of a structure. This can occur due to monotonic loading or cyclic loading and can be sudden and catastrophic. A historical example is the Aberfan disaster. Casagrande referred to this type of phenomena as 'flow liquefaction' although a state of zero effective stress is not required for this to occur.

'Cyclic liquefaction' is the state of soil when large shear strains have accumulated in response to cyclic loading. A typical reference strain for the approximate occurrence of zero effective stress is 5% double amplitude shear strain. This is a soil test-based definition, usually performed via cyclic triaxial, cyclic direct simple shear, or cyclic torsional shear type apparatus. These tests are performed to determine a soil's resistance to liquefaction by observing the number of cycles of loading at a particular shear stress amplitude required to induce 'fails'. Failure here is defined by the aforementioned shear strain criteria.

The term 'cyclic mobility' refers to the mechanism of progressive reduction of effective stress due to cyclic loading. This may occur in all soil types including dense soils. However, on reaching a state of zero effective stress such soils immediately dilate and regain strength. Thus, shear strains are significantly less than a true state of soil liquefaction.

Occurrence

Liquefaction is more likely to occur in loose to moderately saturated granular soils with poor drainage, such as silty sands or sands and gravels containing impermeable sediments. During wave loading, usually cyclic undrained loading, e.g. seismic loading, loose sands tend to decrease in volume, which produces an increase in their pore water pressures and consequently a decrease in shear strength, i.e. reduction in effective stress.

Deposits most susceptible to liquefaction are young (Holocene-age, deposited within the last 10,000 years) sands and silts of similar grain size (well-sorted), in beds at least metres thick, and saturated with water. Such deposits are often found along stream beds, beaches, dunes, and areas where windblown silt (loess) and sand have accumulated. Examples of soil liquefaction include quicksand, quick clay, turbidity currents and earthquake-induced liquefaction.

Depending on the initial void ratio, the soil material can respond to loading either strain-softening or strain-hardening. Strain-softened soils, e.g., loose sands, can be triggered to collapse, either monotonically or cyclically, if the static shear stress is greater than the ultimate or steady-state shear strength of the soil. In this case flow liquefaction occurs, where the soil deforms at a low constant residual shear stress. If the soil strain-hardens, e.g., moderately dense to dense sand, flow liquefaction will generally not occur. However, cyclic softening can occur due to cyclic undrained loading, e.g., earthquake loading. Deformation during cyclic loading depends on the density of the soil, the magnitude and duration of the cyclic loading, and amount of shear stress reversal. If stress reversal occurs, the effective shear stress could reach zero, allowing cyclic liquefaction to take place. If stress reversal does not occur, zero effective stress cannot occur, and cyclic mobility takes place.

The resistance of the cohesionless soil to liquefaction will depend on the density of the soil, confining stresses, soil structure (fabric, age and cementation), the magnitude and duration of the cyclic loading, and the extent to which shear stress reversal occurs.

Liquefaction potential: simplified empirical analysis

Three parameters are needed to assess liquefaction potential using the simplified empirical method:

1. A measure of soil resistance to liquefaction: Standard Penetration Resistance (SPT), Cone Penetration Resistance (CPT), or shear wave velocity (Vs)
2. The earthquake load, measured as cyclic stress ratio ${\displaystyle CSR=\frac{{\tau }_{av}}{{\sigma }_v^{\prime }}=0,65\frac{a_{max}}{g}\frac{{\sigma }_v}{{\sigma }_v^{\prime }}{r}_d}$ 
3. the capacity of the soil to resist liquefaction, expressed in terms of the cyclic resistance ratio (CRR)

Liquefaction potential: advanced constitutive model

The interaction between the solid skeleton and pore fluid flow has been considered by many researchers to model the material softening associated with the liquefaction phenomenon. The dynamic performance of saturated porous media depends on the soil-pore fluid interaction. When the saturated porous media is subjected to strong ground shaking, pore fluid movement relative to the solid skeleton is induced. The transient movement of pore fluid can significantly affect the redistribution of pore water pressure, which is generally governed by the loading rate, soil permeability, pressure gradient, and boundary conditions. It is well known that for a sufficiently high seepage velocity, the governing flow law in porous media is nonlinear and does not follow Darcy's law. This fact has been recently considered in the studies of soil-pore fluid interaction for liquefaction modeling. A fully explicit dynamic finite element method has been developed for turbulent flow law. The governing equations have been expressed for saturated porous media based on the extension of the Biot formulation. The elastoplastic behavior of soil under earthquake loading has been simulated using a generalized plasticity theory that is composed of a yield surface along with a non-associated flow rule.

Earthquake liquefaction

Sand boils that erupted during the 2011 Christchurch earthquake.

Pressures generated during large earthquakes can force underground water and liquefied sand to the surface. This can be observed at the surface as effects known alternatively as "sand boils", "sand blows" or "sand volcanoes". Such earthquake ground deformations can be categorized as primary deformation if located on or close to the ruptured fault, or distributed deformation if located at considerable distance from the ruptured fault.

A liquefaction susceptibility map – excerpt of USGS map for the San Francisco Bay Area. Many areas of concern in this region are also densely urbanized.

The other common observation is land instability – cracking and movement of the ground down slope or towards unsupported margins of rivers, streams, or the coast. The failure of ground in this manner is called 'lateral spreading' and may occur on very shallow slopes with angles only 1 or 2 degrees from the horizontal.

One positive aspect of soil liquefaction is the tendency for the effects of earthquake shaking to be significantly damped (reduced) for the remainder of the earthquake. This is because liquids do not support a shear stress and so once the soil liquefies due to shaking, subsequent earthquake shaking (transferred through ground by shear waves) is not transferred to buildings at the ground surface.

Studies of liquefaction features left by prehistoric earthquakes, called paleoliquefaction or paleoseismology, can reveal information about earthquakes that occurred before records were kept or accurate measurements could be taken.

Soil liquefaction induced by earthquake shaking is a major contributor to urban seismic risk.

Effects

The effects of lateral spreading (River Road in Christchurch following the 2011 Christchurch earthquake)

Damage in Brooklands from the 2010 Canterbury earthquake, where buoyancy caused by soil liquefaction pushed up an underground service including this manhole

The effects of soil liquefaction on the built environment can be extremely damaging. Buildings whose foundations bear directly on sand which liquefies will experience a sudden loss of support, which will result in drastic and irregular settlement of the building causing structural damage, including cracking of foundations and damage to the building structure, or leaving the structure unserviceable, even without structural damage. Where a thin crust of non-liquefied soil exists between building foundation and liquefied soil, a 'punching shear' type foundation failure may occur. Irregular settlement may break underground utility lines. The upward pressure applied by the movement of liquefied soil through the crust layer can crack weak foundation slabs and enter buildings through service ducts and may allow water to damage building contents and electrical services.

Bridges and large buildings constructed on pile foundations may lose support from the adjacent soil and buckle or come to rest at a tilt.

Sloping ground and ground next to rivers and lakes may slide on a liquefied soil layer (termed 'lateral spreading'), opening large ground fissures, and can cause significant damage to buildings, bridges, roads and services such as water, natural gas, sewerage, power and telecommunications installed in the affected ground. Buried tanks and manholes may float in the liquefied soil due to buoyancy. Earth embankments such as flood levees and earth dams may lose stability or collapse if the material comprising the embankment or its foundation liquefies.

Over geological time, liquefaction of soil material due to earthquakes could provide a dense parent material in which the fragipan may develop through pedogenesis.

Mitigation methods

Main article: Dynamic compaction

Mitigation methods have been devised by earthquake engineers and include various soil compaction techniques such as vibro compaction (compaction of the soil by depth vibrators), dynamic compaction, and vibro stone columns. These methods densify soil and enable buildings to avoid soil liquefaction.

Existing buildings can be mitigated by injecting grout into the soil to stabilize the layer of soil that is subject to liquefaction. Another method called IPS (Induced Partial Saturation) is now practicable to apply on larger scale. In this method, the saturation degree of the soil is decreased.

Quicksand

Main article: Quicksand

Quicksand forms when water saturates an area of loose sand, and the sand is agitated. When the water trapped in the batch of sand cannot escape, it creates liquefied soil that can no longer resist force. Quicksand can be formed by standing or (upwards) flowing underground water (as from an underground spring), or by earthquakes. In the case of flowing underground water, the force of the water flow opposes the force of gravity, causing the granules of sand to be more buoyant. In the case of earthquakes, the shaking force can increase the pressure of shallow groundwater, liquefying sand and silt deposits. In both cases, the liquefied surface loses strength, causing buildings or other objects on that surface to sink or fall over.

The saturated sediment may appear quite solid until a change in pressure, or a shock initiates the liquefaction, causing the sand to form a suspension with each grain surrounded by a thin film of water. This cushioning gives quicksand, and other liquefied sediments, a spongy, fluidlike texture. Objects in the liquefied sand sink to the level at which the weight of the object is equal to the weight of the displaced sand/water mix and the object floats due to its buoyancy.

Quick clay

Main article: Quick clay

Quick clay, known as Leda Clay in Canada, is a water-saturated gel, which in its solid form resembles highly sensitive clay. This clay has a tendency to change from a relatively stiff condition to a liquid mass when it is disturbed. This gradual change in appearance from solid to liquid is a process known as spontaneous liquefaction. The clay retains a solid structure despite its high-water content (up to 80% by volume), because surface tension holds water-coated flakes of clay together. When the structure is broken by a shock or sufficient shear, it enters a fluid state.

Quick clay is found only in northern countries such as Russia, Canada, Alaska in the U.S., Norway, Sweden and Finland, which were glaciated during the Pleistocene epoch.

Quick clay has been the underlying cause of many deadly landslides. In Canada alone, it has been associated with more than 250 mapped landslides. Some of these are ancient, and may have been triggered by earthquakes.

Turbidity currents

Main article: Turbidity current

Submarine landslides are turbidity currents and consist of water-saturated sediments flowing downslope. An example occurred during the 1929 Grand Banks earthquake that struck the continental slope off the coast of Newfoundland. Minutes later, transatlantic telephone cables began breaking sequentially, farther and farther downslope, away from the epicenter. Twelve cables were snapped in a total of 28 places. Exact times and locations were recorded for each break. Investigators suggested that a 60-mile-per-hour (100 km/h) submarine landslide or turbidity current of water-saturated sediments swept 400 miles (600 km) down the continental slope from the earthquake's epicenter, snapping the cables as it passed.

Microbiologically induced calcite precipitation

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Microbiologically_induced_calcite_precipitation

 

Microbiologically induced calcium carbonate precipitation (MICP) is a bio-geochemical process that induces calcium carbonate precipitation within the soil matrix. Biomineralization in the form of calcium carbonate precipitation can be traced back to the Precambrian period. Calcium carbonate can be precipitated in three polymorphic forms, which in the order of their usual stabilities are calcite, aragonite and vaterite. The main groups of microorganisms that can induce the carbonate precipitation are photosynthetic microorganisms such as cyanobacteria and microalgae; sulfate-reducing bacteria; and some species of microorganisms involved in nitrogen cycle. Several mechanisms have been identified by which bacteria can induce the calcium carbonate precipitation, including urea hydrolysis, denitrification, sulfate production, and iron reduction. Two different pathways, or autotrophic and heterotrophic pathways, through which calcium carbonate is produced have been identified. There are three autotrophic pathways, which all result in depletion of carbon dioxide and favouring calcium carbonate precipitation. In heterotrophic pathway, two metabolic cycles can be involved: the nitrogen cycle and the sulfur cycle. Several applications of this process have been proposed, such as remediation of cracks and corrosion prevention in concrete, biogrout, sequestration of radionuclides and heavy metals.

Metabolic pathways

Autotrophic pathway

All three principal kinds of bacteria that are involved in autotrophic production of carbonate obtain carbon from gaseous or dissolved carbon dioxide. These pathways include non-methylotrophic methanogenesis, anoxygenic photosynthesis, and oxygenic photosynthesis. Non-methylotrophic methanogenesis is carried out by methanogenic archaebacteria, which use CO₂ and H₂ in anaerobiosis to give CH₄.

Heterotrophic pathway

Two separate and often concurrent heterotrophic pathways that lead to calcium carbonate precipitation may occur, including active and passive carbonatogenesis. During active carbonatogenesis, the carbonate particles are produced by ionic exchanges through the cell membrane by activation of calcium and/or magnesium ionic pumps or channels, probably coupled with carbonate ion production. During passive carbonatogenesis, two metabolic cycles can be involved, the nitrogen cycle and the sulfur cycle. Three different pathways can be involved in the nitrogen cycle: ammonification of amino acids, dissimilatory reduction of nitrate, and degradation of urea or uric acid. In the sulfur cycle, bacteria follow the dissimilatory reduction of sulfate.

Ureolysis or degradation of urea

The microbial urease catalyzes the hydrolysis of urea into ammonium and carbonate. One mole of urea is hydrolyzed intracellularly to 1 mol of ammonia and 1 mole of carbamic acid (1), which spontaneously hydrolyzes to form an additional 1 mole of ammonia and carbonic acid (2).

CO(NH₂)₂ + H₂O → NH₂COOH + NH₃ (1)

NH₂COOH + H₂O → NH₃ + H₂CO₃ (2)

Ammonium and carbonic acid form bicarbonate and 2 moles of ammonium and hydroxide ions in water (3 &4).

2NH₃ + 2H₂O ↔ 2NH⁺₄ +2OH⁻ (3)

H₂CO₃ ↔ HCO⁻₃ + H⁺ (4)

The production of hydroxide ions results in the increase of pH, which in turn can shift the bicarbonate equilibrium, resulting in the formation of carbonate ions (5)

HCO⁻₃ + H⁺ + 2NH⁺₄ +2OH⁻ ↔ CO₃⁻² + 2NH⁺₄ + 2H₂O (5)

The produced carbonate ions precipitate in the presence of calcium ions as calcium carbonate crystals (6).

Ca⁺² + CO₃⁻² ↔ CaCO₃ (6)

The formation of a monolayer of calcite further increases the affinity of the bacteria to the soil surface, resulting in the production of multiple layers of calcite.

Possible applications

Material science

MICP has been reported as a long-term remediation technique that has been exhibited high potential for crack cementation of various structural formations such as granite and concrete.

Treatment of concrete

MICP has been shown to prolong concrete service life due to calcium carbonate precipitation. The calcium carbonate heals the concrete by solidifying on the cracked concrete surface, mimicking the process by which bone fractures in human body are healed by osteoblast cells that mineralize to reform the bone. Two methods are currently being studied: injection of calcium carbonate precipitating bacteria. and by applying bacteria and nutrients as a surface treatment. Increase in strength and durability of MICP treated cement mortar and concrete has been reported.

Precast materials (tiles, bricks, etc.)

Architect Ginger Krieg Dosier won the 2010 Metropolis Next Generation Design Competition for her work using microbial-induced calcite precipitation to manufacture bricks while lowering carbon dioxide emissions. She has since founded Biomason, Inc., a company that employs microorganisms and chemical processes to manufacture building materials.

Fillers for rubber, plastics and ink

MICP technique may be applied to produce a material that can be used as a filler in rubber and plastics, fluorescent particles in stationery ink, and a fluorescent marker for biochemistry applications, such as western blot.

Liquefaction prevention

Microbial induced calcium carbonate precipitation has been proposed as an alternative cementation technique to improve the properties of potentially liquefiable sand. The increase in shear strength, confined compressive strength, stiffness and liquefaction resistance was reported due to calcium carbonate precipitation resulting from microbial activity. The increase of soil strength from MICP is a result of the bonding of the grains and the increased density of the soil. Research has shown a linear relationship between the amount of carbonate precipitation and the increase in strength and porosity. A 90% decrease in porosity has also been observed in MICP treated soil. Light microscopic imaging suggested that the mechanical strength enhancement of cemented sandy material is caused mostly due to point-to-point contacts of calcium carbonate crystals and adjacent sand grains.

One-dimensional column experiments allowed the monitoring of treatment progration by the means of change in pore fluid chemistry. Triaxial compression tests on untreated and bio-cemented Ottawa sand have shown an increase in shear strength by a factor of 1.8. Changes in pH and concentrations of urea, ammonium, calcium and calcium carbonate in pore fluid with the distance from the injection point in 5-meter column experiments have shown that bacterial activity resulted in successful hydrolysis of urea, increase in pH and precipitation of calcite. However, such activity decreased as the distance from the injection point increased. Shear wave velocity measurements demonstrated that positive correlation exists between shear wave velocity and the amount of precipitated calcite.

One of the first patents on ground improvement by MICP was the patent “Microbial Biocementation” by Murdoch University (Australia). A large scale (100 m³) have shown a significant increase in shear wave velocity was observed during the treatment. Originally MICP was tested and designed for underground applications in water saturated ground, requiring injection and production pumps. Recent work ^[51] has demonstrated that surface percolation or irrigation is also feasible and in fact provides more strength per amount of calcite provided because crystals form more readily at the bridging points between sand particles over which the water percolates.

Benefits of MICP for liquefaction prevention

MICP has the potential to be a cost-effective and green alternative to traditional methods of stabilizing soils, such as chemical grouting, which typically involve the injection of synthetic materials into the soil. These synthetic additives are typically costly and can create environmental hazards by modifying the pH and contaminating soils and groundwater. Excluding sodium silicate, all traditional chemical additives are toxic. Soils engineered with MICP meet green construction requirements because the process exerts minimal disturbance to the soil and the environment.

Possible limitations of MICP as a cementation technique

MICP treatment may be limited to deep soil due to limitations of bacterial growth and movement in subsoil. MICP may be limited to the soils containing limited amounts of fines due to the reduction in pore spaces in fine soils. Based on the size of microorganism, the applicability of biocementation is limited to GW, GP, SW, SP, ML, and organic soils. Bacteria are not expected to enter through pore throats smaller than approximately 0.4 µm. In general, the microbial abundance was found to increase with the increase in particle size. On the other hand, the fine particles may provide more favorable nucleation sites for calcium carbonate precipitation because the mineralogy of the grains could directly influence the thermodynamics of the precipitation reaction in the system. The habitable pores and traversable pore throats were found in coarse sediments and some clayey sediments at shallow depth. In clayey soil, bacteria are capable of reorienting and moving clay particles under low confining stress (at shallow depths). However, inability to make these rearrangements under high confining stresses limits bacterial activity at larger depths. Furthermore, sediment-cell interaction may cause puncture or tensile failure of the cell membrane. Similarly, at larger depths, silt and sand particles may crush and cause a reduction in pore spaces, reducing the biological activity. Bacterial activity is also impacted by challenges such as predation, competition, pH, temperature, and nutrient availability. These factors can contribute to the population decline of bacteria. Many of these limitations can be overcome through the use of MICP through bio-stimulation - a process through which indigenous ureolytic soil bacteria are enriched in situ. This method is not always possible as not all indigenous soils have enough ureolytic bacteria to achieve successful MICP.

Remediation for heavy metal and radionuclide contamination

MICP is a promising technique that can be used for containment of various contaminants and heavy metals. The availability of lead in soil may reduced by its chelation with the MICP product, which is the mechanism responsible for lead immobilization. MICP can be also applied to achieve sequestration of heavy metals and radionuclides. Microbially induced calcium carbonate precipitation of radionuclide and contaminant metals into calcite is a competitive co-precipitation reaction in which suitable divalent cations are incorporated into the calcite lattice. Europium, a trivalent lanthanide, which was used as a homologue for trivalent actinides, such as Pu(III), Am(III), and Cm(III), was shown to incorporate into the calcite phase substituting for Ca(II) as well as in a low-symmetry site within the biomineral.

Prevention

Shewanella oneidensis inhibits the dissolution of calcite under laboratory conditions.

Biomineralization

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Biomineralization

Biomineralization, also written biomineralisation, is the process by which living organisms produce minerals, often resulting in hardened or stiffened mineralized tissues. It is an extremely widespread phenomenon: all six taxonomic kingdoms contain members that are able to form minerals, and over 60 different minerals have been identified in organisms. Examples include silicates in algae and diatoms, carbonates in invertebrates, and calcium phosphates and carbonates in vertebrates. These minerals often form structural features such as sea shells and the bone in mammals and birds.

Organisms have been producing mineralized skeletons for the past 550 million years. Calcium carbonates and calcium phosphates are usually crystalline, but silica organisms (sponges, diatoms...) are always non-crystalline minerals. Other examples include copper, iron, and gold deposits involving bacteria. Biologically formed minerals often have special uses such as magnetic sensors in magnetotactic bacteria (Fe₃O₄), gravity-sensing devices (CaCO₃, CaSO₄, BaSO₄) and iron storage and mobilization (Fe₂O₃•H₂O in the protein ferritin).

In terms of taxonomic distribution, the most common biominerals are the phosphate and carbonate salts of calcium that are used in conjunction with organic polymers such as collagen and chitin to give structural support to bones and shells. The structures of these biocomposite materials are highly controlled from the nanometer to the macroscopic level, resulting in complex architectures that provide multifunctional properties. Because this range of control over mineral growth is desirable for materials engineering applications, there is interest in understanding and elucidating the mechanisms of biologically-controlled biomineralization.

Types

Mineralization can be subdivided into different categories depending on the following: the organisms or processes that create chemical conditions necessary for mineral formation, the origin of the substrate at the site of mineral precipitation, and the degree of control that the substrate has on crystal morphology, composition, and growth. These subcategories include biomineralization, organomineralization, and inorganic mineralization, which can be subdivided further. However, the usage of these terms varies widely in the scientific literature because there are no standardized definitions. The following definitions are based largely on a paper written by Dupraz et al. (2009), which provided a framework for differentiating these terms.

Biomineralization

Biomineralization, biologically controlled mineralization, occurs when crystal morphology, growth, composition, and location are completely controlled by the cellular processes of a specific organism. Examples include the shells of invertebrates, such as molluscs and brachiopods. Additionally, the mineralization of collagen provides crucial compressive strength for the bones, cartilage, and teeth of vertebrates.

Organomineralization

This type of mineralization includes both biologically induced mineralization and biologically influenced mineralization.

Living Stromatolites in Exumas, Bahamas.

Fossil skeletal parts from extinct belemnite cephalopods of the Jurassic – these contain mineralized calcite and aragonite.

• Biologically induced mineralization occurs when the metabolic activity of microbes (e.g. bacteria) produces chemical conditions favorable for mineral formation. The substrate for mineral growth is the organic matrix, secreted by the microbial community, and affects crystal morphology and composition. Examples of this type of mineralization include calcareous or siliceous stromatolites and other microbial mats. A more specific type of biologically induced mineralization, remote calcification or remote mineralization, takes place when calcifying microbes occupy a shell-secreting organism and alter the chemical environment surrounding the area of shell formation. The result is mineral formation not strongly controlled by the cellular processes of the animal host (i.e., remote mineralization); this may lead to unusual crystal morphologies.
• Biologically influenced mineralization takes place when chemical conditions surrounding the site of mineral formation are influenced by abiotic processes (e.g., evaporation or degassing). However, the organic matrix (secreted by microorganisms) is responsible for crystal morphology and composition. Examples include micro- to nanometer-scale crystals of various morphologies.

Biological mineralization can also take place as a result of fossilization. See also calcification.

Biological roles

Among animals, biominerals composed of calcium carbonate, calcium phosphate, or silica perform a variety of roles such as support, defense, and feeding.

• 
  Many protists, like this coccolithophore, have protective mineralised shells
   
• 
  Forams from a beach
• 
  Many invertebrate animals have external exoskeletons or shells, which achieve rigidity by a variety of mineralisations
   
• 
  Vertebrate animals have internal endoskeletons which achieve rigidity by binding calcium phosphate into hydroxylapatite

If present on a supracellular scale, biominerals are usually deposited by a dedicated organ, which is often defined very early in embryological development. This organ will contain an organic matrix that facilitates and directs the deposition of crystals. The matrix may be collagen, as in deuterostomes, or based on chitin or other polysaccharides, as in molluscs.

In molluscs

Further information: Mollusc shell

A variety of mollusc shells

The mollusc shell is a biogenic composite material that has been the subject of much interest in materials science because of its unusual properties and its model character for biomineralization. Molluscan shells consist of 95–99% calcium carbonate by weight, while an organic component makes up the remaining 1–5%. The resulting composite has a fracture toughness ≈3000 times greater than that of the crystals themselves. In the biomineralization of the mollusc shell, specialized proteins are responsible for directing crystal nucleation, phase, morphology, and growths dynamics and ultimately give the shell its remarkable mechanical strength. The application of biomimetic principles elucidated from mollusc shell assembly and structure may help in fabricating new composite materials with enhanced optical, electronic, or structural properties.

The most described arrangement in mollusc shells is the nacre, known in large shells such as Pinna or the pearl oyster (Pinctada). Not only does the structure of the layers differ, but so do their mineralogy and chemical composition. Both contain organic components (proteins, sugars, and lipids), and the organic components are characteristic of the layer and of the species. The structures and arrangements of mollusc shells are diverse, but they share some features: the main part of the shell is crystalline calcium carbonate (aragonite, calcite), though some amorphous calcium carbonate occurs as well; and although they react as crystals, they never show angles and facets.

In fungi

Global involvement of fungi in some biogeochemical cycles 

 

(a) Fungi contribute substantially to mineral weathering, leading to the release of bioavailable metals or nutrients, which eventually may be uptaken by living organisms or precipitated as secondary minerals
(b) Fungi as heterotrophs, recycle organic matter. While doing so, they produce metabolites such as organic acids that can also precipitate as secondary minerals (salts). Recycling organic matter eventually releases constitutive elements such as C, N, P, and S
(c) CO₂ produced by heterotrophic fungal respiration can dissolve into H₂O and depending on the physicochemical conditions precipitate as CaCO₃ leading to the formation of a secondary mineral.

Fungi are a diverse group of organisms that belong to the eukaryotic domain. Studies of their significant roles in geological processes, "geomycology", have shown that fungi are involved with biomineralization, biodegradation, and metal-fungal interactions.

In studying fungi's roles in biomineralization, it has been found that fungi deposit minerals with the help of an organic matrix, such as a protein, that provides a nucleation site for the growth of biominerals. Fungal growth may produce a copper-containing mineral precipitate, such as copper carbonate produced from a mixture of (NH₄)₂CO₃ and CuCl₂. The production of the copper carbonate is produced in the presence of proteins made and secreted by the fungi. These fungal proteins that are found extracellularly aid in the size and morphology of the carbonate minerals precipitated by the fungi.

In addition to precipitating carbonate minerals, fungi can also precipitate uranium-containing phosphate biominerals in the presence of organic phosphorus that acts as a substrate for the process. The fungi produce a hyphal matrix, also known as mycelium, that localizes and accumulates the uranium minerals that have been precipitated. Although uranium is often deemed as toxic to living organisms, certain fungi such as Aspergillus niger and Paecilomyces javanicus can tolerate it.

Though minerals can be produced by fungi, they can also be degraded, mainly by oxalic acid–producing strains of fungi. Oxalic acid production is increased in the presence of glucose for three organic acid producing fungi: Aspergillus niger, Serpula himantioides, and Trametes versicolor. These fungi have been found to corrode apatite and galena minerals. Degradation of minerals by fungi is carried out through a process known as neogenesis. The order of most to least oxalic acid secreted by the fungi studied are Aspergillus niger, followed by Serpula himantioides, and finally Trametes versicolor.

In bacteria

It is less clear what purpose biominerals serve in bacteria. One hypothesis is that cells create them to avoid entombment by their own metabolic byproducts. Iron oxide particles may also enhance their metabolism.

Other roles

The chalk of the White Cliffs of Dover is almost entirely formed from fossil skeleton remains (coccoliths), biomineralized by planktonic microorganisms (coccolithophores)

Biomineralization plays significant global roles terraforming the planet, as well as in biogeochemical cycles  and as a carbon sink.

Composition

Most biominerals can be grouped by chemical composition into one of three distinct mineral classes: silicates, carbonates, or phosphates.

Silicates

A testate amoeba which has covered itself with protective diatom frustules

Peacock mantis shrimp smash their prey by swinging club-like raptorial claws made of hydroxyapatite 

Silicates (glass) are common in marine biominerals, where diatoms and radiolaria form frustules from hydrated amorphous silica (opal).

Carbonates

The major carbonate in biominerals is CaCO₃. The most common polymorphs in biomineralization are calcite (e.g. foraminifera, coccolithophores) and aragonite (e.g. corals), although metastable vaterite and amorphous calcium carbonate can also be important, either structurally or as intermediate phases in biomineralization. Some biominerals include a mixture of these phases in distinct, organised structural components (e.g. bivalve shells). Carbonates are particularly prevalent in marine environments, but also present in freshwater and terrestrial organisms.

Phosphates

The most common biogenic phosphate is hydroxyapatite (HA), a calcium phosphate (Ca₁₀(PO₄)₆(OH)₂) and a naturally occurring form of apatite. It is a primary constituent of bone, teeth, and fish scales. Bone is made primarily of HA crystals interspersed in a collagen matrix—65 to 70% of the mass of bone is HA. Similarly, HA is 70 to 80% of the mass of dentin and enamel in teeth. In enamel, the matrix for HA is formed by amelogenins and enamelins instead of collagen. Remineralisation of tooth enamel involves the reintroduction of mineral ions into demineralised enamel. Hydroxyapatite is the main mineral component of enamel in teeth. During demineralisation, calcium and phosphorus ions are drawn out from the hydroxyapatite. The mineral ions introduced during remineralisation restore the structure of the hydroxyapatite crystals.

The clubbing appendages of the peacock mantis shrimp are made of an extremely dense form of the mineral which has a higher specific strength; this has led to its investigation for potential synthesis and engineering use. Their dactyl appendages have excellent impact resistance due to the impact region being composed of mainly crystalline hydroxyapatite, which offers significant hardness. A periodic layer underneath the impact layer composed of hydroxyapatite with lower calcium and phosphorus content (thus resulting in a much lower modulus) inhibits crack growth by forcing new cracks to change directions. This periodic layer also reduces the energy transferred across both layers due to the large difference in modulus, even reflecting some of the incident energy.

Glomerula piloseta (Sabellidae), longitudinal section of the tube showing aragonitic spherulitic prismatic structure

Composition	Example organisms
Calcium carbonate (calcite or aragonite)	Foraminifera Coccolithophores Calcareous sponge spicules Corals Archaeocyatha Bryozoans Brachiopod and mollusc shells Echinoderms Serpulidae
Silica (silicate/glass/opal)	Radiolarians Diatoms Most sponge spicules
Apatite (phosphate minerals)	Enamel (vertebrate teeth) Vertebrate bone Conodonts Linguliform brachiopod shells

Other minerals

Beyond these main three categories, there are a number of less common types of biominerals, usually resulting from a need for specific physical properties or the organism inhabiting an unusual environment. For example, teeth that are primarily used for scraping hard substrates may be reinforced with particularly tough minerals, such as the iron minerals magnetite in chitons or goethite in limpets. Gastropod molluscs living close to hydrothermal vents reinforce their carbonate shells with the iron-sulphur minerals pyrite and greigite. Magnetotactic bacteria also employ magnetic iron minerals magnetite and greigite to produce magnetosomes to aid orientation and distribution in the sediments.

Magnetotactic bacterium containing a chain of magnetosomes

 

Magnetosome chain with octahedral habits modelled lower right

• 
  Chitons have aragonite shells and aragonite-based eyes, as well as teeth coated with magnetite.
   
• 
  Limpets have carbonate shells and teeth reinforced with goethite

• 
  Acantharian radiolarians have celestine crystal shells
• 
  Celestine crystals, the heaviest mineral in the oceans

Celestine, the heaviest mineral in the ocean, consists of strontium sulfate, SrSO₄. The mineral is named for the delicate blue colour of its crystals. Planktic acantharean radiolarians form celestine crystal shells. The denseness of the celestite ensures their shells function as mineral ballast, resulting in fast sedimentation to bathypelagic depths. High settling fluxes of acantharian cysts have been observed at times in the Iceland Basin and the Southern Ocean, as much as half of the total gravitational organic carbon flux.

Diversity

The most widespread biomineral is silica

The siliceous diatom frustule has the highest strength of any known biological material

 

Sponge spicules, like this from a siliceous glass sponge, form structures many times more flexible than equivalent structures made of pure silica

 

Transparent glass test or shell of a radiolarian

In nature, there is a wide array of biominerals, ranging from iron oxide to strontium sulfate, with calcareous biominerals being particularly notable. However, the most taxonomically widespread biomineral is silica (SiO₂·nH₂O), being present in all eukaryotic supergroups. Notwithstanding, the degree of silicification can vary even between closely related taxa, from being found in composite structures with other biominerals (e.g., limpet teeth; to forming minor structures (e.g., ciliate granules; or being a major structural constituent of the organism. The most extreme degree of silicification is evident in the diatoms, where almost all species have an obligate requirement for silicon to complete cell wall formation and cell division. Biogeochemically and ecologically, diatoms are the most important silicifiers in modern marine ecosystems, with radiolarians (polycystine and phaeodarian rhizarians), silicoflagellates (dictyochophyte and chrysophyte stramenopiles), and sponges with prominent roles as well. In contrast, the major silicifiers in terrestrial ecosystems are the land plants (embryophytes), with other silicifying groups (e.g., testate amoebae) having a minor role.

Broadly, biomineralized structures evolve and diversify when the energetic cost of biomineral production is less than the expense of producing an equivalent organic structure. The energetic costs of forming a silica structure from silicic acid are much less than forming the same volume from an organic structure (≈20-fold less than lignin or 10-fold less than polysaccharides like cellulose). Based on a structural model of biogenic silica, Lobel et al. (1996) identified by biochemical modeling a low-energy reaction pathway for nucleation and growth of silica. The combination of organic and inorganic components within biomineralized structures often results in enhanced properties compared to exclusively organic or inorganic materials. With respect to biogenic silica, this can result in the production of much stronger structures, such as siliceous diatom frustules having the highest strength per unit density of any known biological material, or sponge spicules being many times more flexible than an equivalent structure made of pure silica. As a result, biogenic silica structures are used for support, feeding, predation defense  and environmental protection as a component of cyst walls. Biogenic silica also has useful optical properties for light transmission and modulation in organisms as diverse as plants, diatoms, sponges, and molluscs. There is also evidence that silicification is used as a detoxification response in snails  and plants, biosilica has even been suggested to play a role as a pH buffer for the enzymatic activity of carbonic anhydrase, aiding the acquisition of inorganic carbon for photosynthesis.

• 
  Diversity of biomineralization across the eukaryotes 

  The phylogeny shown in this diagram is based on Adl et al. (2012), with major eukaryotic supergroups named in boxes. Letters next to taxon names denote the presence of biomineralization, with circled letters indicating the prominent and widespread use of that biomineral. S, silica; C, calcium carbonate; P, calcium phosphate; I, iron (magnetite/goethite); X, calcium oxalate; SO₄, sulfates (calcium/barium/strontium), ? denotes uncertainty in the report.

There are questions which have yet to be resolved, such as why some organisms biomineralize while others do not, and why is there such a diversity of biominerals besides silicon when silicon is so abundant, comprising 28% of the Earth's crust. The answer to these questions lies in the evolutionary interplay between biomineralization and geochemistry, and in the competitive interactions that have arisen from these dynamics. Fundamentally whether an organism produces silica or not involves evolutionary trade-offs and competition between silicifiers themselves, and non-silicifying organisms (both those which use other biominerals, and non-mineralizing groups). Mathematical models and controlled experiments of resource competition in phytoplankton have demonstrated the rise to dominance of different algal species based on nutrient backgrounds in defined media. These have been part of fundamental studies in ecology. However, the vast diversity of organisms that thrive in a complex array of biotic and abiotic interactions in oceanic ecosystems are a challenge to such minimal models and experimental designs, whose parameterization and possible combinations, respectively, limit the interpretations that can be built on them.

Evolution

Some calcareous sponges (Ernst Haeckel, Kunstformen der Natur).

The first evidence of biomineralization dates to some 750 million years ago, and sponge-grade organisms may have formed calcite skeletons 630 million years ago. But in most lineages, biomineralization first occurred in the Cambrian or Ordovician periods. Organisms used whichever form of calcium carbonate was more stable in the water column at the point in time when they became biomineralized, and stuck with that form for the remainder of their biological history (but see for a more detailed analysis). The stability is dependent on the Ca/Mg ratio of seawater, which is thought to be controlled primarily by the rate of sea floor spreading, although atmospheric CO₂ levels may also play a role.

Biomineralization evolved multiple times, independently, and most animal lineages first expressed biomineralized components in the Cambrian period. Many of the same processes are used in unrelated lineages, which suggests that biomineralization machinery was assembled from pre-existing "off-the-shelf" components already used for other purposes in the organism. Although the biomachinery facilitating biomineralization is complex – involving signalling transmitters, inhibitors, and transcription factors – many elements of this 'toolkit' are shared between phyla as diverse as corals, molluscs, and vertebrates. The shared components tend to perform quite fundamental tasks, such as designating that cells will be used to create the minerals, whereas genes controlling more finely tuned aspects that occur later in the biomineralization process, such as the precise alignment and structure of the crystals produced, tend to be uniquely evolved in different lineages. This suggests that Precambrian organisms were employing the same elements, albeit for a different purpose – perhaps to avoid the inadvertent precipitation of calcium carbonate from the supersaturated Proterozoic oceans. Forms of mucus that are involved in inducing mineralization in most animal lineages appear to have performed such an anticalcifatory function in the ancestral state. Further, certain proteins that would originally have been involved in maintaining calcium concentrations within cells are homologous in all animals, and appear to have been co-opted into biomineralization after the divergence of the animal lineages. The galaxins are one probable example of a gene being co-opted from a different ancestral purpose into controlling biomineralization, in this case, being 'switched' to this purpose in the Triassic scleractinian corals; the role performed appears to be functionally identical to that of the unrelated pearlin gene in molluscs. Carbonic anhydrase serves a role in mineralization broadly in the animal kingdom, including in sponges, implying an ancestral role. Far from being a rare trait that evolved a few times and remained stagnant, biomineralization pathways in fact evolved many times and are still evolving rapidly today; even within a single genus, it is possible to detect great variation within a single gene family.

The homology of biomineralization pathways is underlined by a remarkable experiment whereby the nacreous layer of a molluscan shell was implanted into a human tooth, and rather than experiencing an immune response, the molluscan nacre was incorporated into the host bone matrix. This points to the exaptation of an original biomineralization pathway. The biomineralisation capacity of brachiopods and molluscs has also been demonstrated to be homologous, building on a conserved set of genes. This indicates that biomineralisation is likely ancestral to all lophotrochozoans.

The most ancient example of biomineralization, dating back 2 billion years, is the deposition of magnetite, which is observed in some bacteria, as well as the teeth of chitons and the brains of vertebrates; it is possible that this pathway, which performed a magnetosensory role in the common ancestor of all bilaterians, was duplicated and modified in the Cambrian to form the basis for calcium-based biomineralization pathways. Iron is stored in close proximity to magnetite-coated chiton teeth, so that the teeth can be renewed as they wear. Not only is there a marked similarity between the magnetite deposition process and enamel deposition in vertebrates, but some vertebrates even have comparable iron storage facilities near their teeth.

Potential applications

Most traditional approaches to the synthesis of nanoscale materials are energy inefficient, requiring stringent conditions (e.g., high temperature, pressure, or pH), and often produce toxic byproducts. Furthermore, the quantities produced are small, and the resultant material is usually irreproducible because of the difficulties in controlling agglomeration. In contrast, materials produced by organisms have properties that usually surpass those of analogous synthetically manufactured materials with similar phase composition. Biological materials are assembled in aqueous environments under mild conditions by using macromolecules. Organic macromolecules collect and transport raw materials and assemble these substrates and into short- and long-range ordered composites with consistency and uniformity.

The aim of biomimetics is to mimic the natural way of producing minerals such as apatites. Many man-made crystals require elevated temperatures and strong chemical solutions, whereas the organisms have long been able to lay down elaborate mineral structures at ambient temperatures. Often, the mineral phases are not pure but are made as composites that entail an organic part, often protein, which takes part in and controls the biomineralization. These composites are often not only as hard as the pure mineral but also tougher, as the micro-environment controls biomineralization.

Architecture

• 
  Bacillus megaterium
   
• 
  Bacillus subtilis

One biological system that might be of key importance in the future development of architecture is bacterial biofilm. The term biofilm refers to complex heterogeneous structures comprising different populations of microorganisms that attach and form a community on inert (e.g. rocks, glass, plastic) or organic (e.g. skin, cuticle, mucosa) surfaces.

The properties of the surface, such as charge, hydrophobicity and roughness, determine initial bacterial attachment. A common principle of all biofilms is the production of extracellular matrix (ECM) composed of different organic substances, such as extracellular proteins, exopolysaccharides and nucleic acids. While the ability to generate ECM appears to be a common feature of multicellular bacterial communities, the means by which these matrices are constructed and function are diverse.

• 
  Model for biomineralization‐mediated scaffolding
  of bacterial biofilms

  A directed growth of the calcium carbonate crystals allows mechanical support of the 3D structure. The bacterial extracellular matrix (brown) promotes the crystals' growth in specific directions.

Bacterially induced calcium carbonate precipitation can be used to produce "self‐healing" concrete. Bacillus megaterium spores and suitable dried nutrients are mixed and applied to steel‐reinforced concrete. When the concrete cracks, water ingress dissolves the nutrients and the bacteria germinate triggering calcium carbonate precipitation, resealing the crack and protecting the steel reinforcement from corrosion. This process can also be used to manufacture new hard materials, such as bio‐cement.

However, the full potential of bacteria‐driven biomineralization is yet to be realized, as it is currently used as a passive filling rather than as a smart designable material. A future challenge is to develop ways to control the timing and the location of mineral formation, as well as the physical properties of the mineral itself, by environmental input. Bacillus subtilis has already been shown to respond to its environment, by changing the production of its ECM. It uses the polymers produced by single cells during biofilm formation as a physical cue to coordinate ECM production by the bacterial community.

Uranium contaminants

• 
  Autunite crystal

Biomineralization may be used to remediate groundwater contaminated with uranium. The biomineralization of uranium primarily involves the precipitation of uranium phosphate minerals associated with the release of phosphate by microorganisms. Negatively charged ligands at the surface of the cells attract the positively charged uranyl ion (UO₂²⁺). If the concentrations of phosphate and UO₂²⁺ are sufficiently high, minerals such as autunite (Ca(UO₂)₂(PO₄)₂•10-12H₂O) or polycrystalline HUO₂PO₄ may form thus reducing the mobility of UO₂²⁺. Compared to the direct addition of inorganic phosphate to contaminated groundwater, biomineralization has the advantage that the ligands produced by microbes will target uranium compounds more specifically rather than react actively with all aqueous metals. Stimulating bacterial phosphatase activity to liberate phosphate under controlled conditions limits the rate of bacterial hydrolysis of organophosphate and the release of phosphate to the system, thus avoiding clogging of the injection location with metal phosphate minerals. The high concentration of ligands near the cell surface also provides nucleation foci for precipitation, which leads to higher efficiency than chemical precipitation.

Biogenic mineral controversy

See also: Mineral § Biogenic minerals

The geological definition of mineral normally excludes compounds that occur only in living beings. However, some minerals are often biogenic (such as calcite) or are organic compounds in the sense of chemistry (such as mellite). Moreover, living beings often synthesize inorganic minerals (such as hydroxylapatite) that also occur in rocks.

The International Mineralogical Association (IMA) is the generally recognized standard body for the definition and nomenclature of mineral species. As of December 2020, the IMA recognizes 5,650 official mineral species out of 5,862 proposed or traditional ones.

A topic of contention among geologists and mineralogists has been the IMA's decision to exclude biogenic crystalline substances. For example, Lowenstam (1981) stated that "organisms are capable of forming a diverse array of minerals, some of which cannot be formed inorganically in the biosphere."

Skinner (2005) views all solids as potential minerals and includes biominerals in the mineral kingdom, which are those that are created by the metabolic activities of organisms. Skinner expanded the previous definition of a mineral to classify "element or compound, amorphous or crystalline, formed through biogeochemical processes," as a mineral.

Recent advances in high-resolution genetics and X-ray absorption spectroscopy are providing revelations on the biogeochemical relations between microorganisms and minerals that may shed new light on this question. For example, the IMA-commissioned "Working Group on Environmental Mineralogy and Geochemistry " deals with minerals in the hydrosphere, atmosphere, and biosphere. The group's scope includes mineral-forming microorganisms, which exist on nearly every rock, soil, and particle surface spanning the globe to depths of at least 1,600 metres below the sea floor and 70 kilometres into the stratosphere (possibly entering the mesosphere).

Biogeochemical cycles have contributed to the formation of minerals for billions of years. Microorganisms can precipitate metals from solution, contributing to the formation of ore deposits. They can also catalyze the dissolution of minerals.

Prior to the International Mineralogical Association's listing, over 60 biominerals had been discovered, named, and published. These minerals (a sub-set tabulated in Lowenstam (1981)) are considered minerals proper according to Skinner's (2005) definition. These biominerals are not listed in the International Mineral Association official list of mineral names, however, many of these biomineral representatives are distributed amongst the 78 mineral classes listed in the Dana classification scheme.

Skinner's (2005) definition of a mineral takes this matter into account by stating that a mineral can be crystalline or amorphous. Although biominerals are not the most common form of minerals, they help to define the limits of what constitutes a mineral properly. Nickel's (1995) formal definition explicitly mentioned crystallinity as a key to defining a substance as a mineral. A 2011 article defined icosahedrite, an aluminium-iron-copper alloy as mineral; named for its unique natural icosahedral symmetry, it is a quasicrystal. Unlike a true crystal, quasicrystals are ordered but not periodic.

List of minerals

Examples of biogenic minerals include:

• Apatite in bones and teeth.
• Aragonite, calcite, fluorite in vestibular systems (part of the inner ear) of vertebrates.
• Aragonite and calcite in travertine and biogenic silica (siliceous sinter, opal) deposited through algal action.
• Hydroxylapatite formed by mitochondria.
• Magnetite and greigite formed by magnetotactic bacteria.
• Pyrite and marcasite in sedimentary rocks deposited by sulfate-reducing bacteria.
• Quartz formed from bacterial action on fossil fuels (gas, oil, coal).
• Goethite found as filaments in limpet teeth.

Astrobiology

It has been suggested that biominerals could be important indicators of extraterrestrial life and thus could play an important role in the search for past or present life on Mars. Furthermore, organic components (biosignatures) that are often associated with biominerals are believed to play crucial roles in both pre-biotic and biotic reactions.

On 24 January 2014, NASA reported that current studies by the Curiosity and Opportunity rovers on the planet Mars will now be searching for evidence of ancient life, including a biosphere based on autotrophic, chemotrophic and/or chemolithoautotrophic microorganisms, as well as ancient water, including fluvio-lacustrine environments (plains related to ancient rivers or lakes) that may have been habitable. The search for evidence of habitability, taphonomy (related to fossils), and organic carbon on the planet Mars is now a primary NASA objective.