Biomineralization

thumb|upright=1.2|Fossil skeletal parts from extinct [[Belemnitida|belemnite cephalopods of the Jurassic – these contain mineralized calcite and aragonite.]]

Biomineralization, also written biomineralisation, is the process by which living organisms produce minerals, 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.

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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. 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. and sponge-grade organisms may have formed calcite skeletons . 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, (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 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. 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 most ancient example of biomineralization, dating back 2&nbsp;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.

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.

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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. 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.

Biogenic mineral controversy

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. , the IMA recognizes 5,650 official mineral species out of 5,862 proposed or traditional ones.

The IMA's decision to exclude biogenic crystalline substances is a topic of contention among geologists and mineralogists. 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 created by organisms' metabolic activities. Skinner expanded the previous definition of a mineral to classify "element or compound, amorphous or crystalline, formed through biogeochemical processes," as a mineral. 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.

Before the International Mineralogical Association's listing, over 60 biominerals had been discovered, named, and published. These minerals (a sub-set tabulated in Lowenstam (1981) however, many of these biomineral representatives are distributed among the 78 mineral classes listed in the Dana classification scheme. 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.

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
• Goethite found as filaments in limpet teeth
• Hydroxyapatite formed by mitochondria
• Magnetite and greigite formed by magnetotactic bacteria
• Oxalate and calcium carbonate raphides, silica bodies, strontium and barium sulfate in some plants
• Pyrite and marcasite in sedimentary rocks deposited by sulfate-reducing bacteria
• Quartz formed from bacterial action on fossil fuels (gas, oil, coal)

Astrobiology

Biominerals could be important indicators of extraterrestrial life and thus could play an essential 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 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.