Biomineralization

Life and minerals are more deeply intertwined than most introductory treatments of mineralogy suggest. Biomineralization refers specifically to the processes by which organisms are directly involved in mineral growth - not the indirect environmental effects of life, such as the Great Oxidation Event’s creation of oxidising conditions for weathering minerals, but the direct participation of living organisms in precipitating and building mineral material. ^[1] About 110 biominerals and mineraloids have been identified across all major chemical groups - carbonates, phosphates, sulfates, sulfides, oxides, halides, silicates, and organic minerals - and the organisms involved span more than 55 phyla across all five kingdoms of life. ^[1]

Biomineralization divides into two broad categories that differ in the degree of biological control over the mineralisation process. ^[1]

Biologically Induced Mineralization

Biologically induced mineralization involves mineral precipitation as a consequence of an organism’s interaction with the surrounding aqueous environment, or as a by-product of metabolic activity. The same thermodynamic requirements apply as for any other mineral growth - the right chemical elements must be present, the mineral must be more stable than its precursors, and nucleation must be possible - but biological activity provides the trigger. ^[1]

Two mechanisms operate. First, cells can passively provide nucleation sites. Cell surfaces carry an abundance of positively and negatively charged sites (ligands) that attract and hold ions of the appropriate charge. The spacing of these charges on the cell surface determines which ions are preferentially sorbed, making the process geometrically similar to epitaxial nucleation on a mineral surface. Second, cells can metabolically alter the local chemical environment - changing pH, redox conditions, or ion concentrations - to bring the surrounding solution into a state where mineral precipitation is thermodynamically favoured. ^[1]

Iron Hydroxide Precipitation

The simplest biologically induced iron mineralisation involves Fe²⁺-bearing water reacting with dissolved oxygen to precipitate ferrihydrite (5Fe₂O₃·9H₂O). Bacteria in the water provide heterogeneous nucleation sites, triggering precipitation of this ochre-coloured material that is one of the primary constituents of limonite. ^[1]

Chlorobium ferrooxidans provides a metabolic example: this photosynthetic bacterium oxidises Fe²⁺ to Fe³⁺ as part of its metabolism, and the resulting Fe³⁺ then combines with oxygen and water to precipitate as ferric hydroxide. This process produces bog iron in iron-rich springs - a material historically important as an iron ore in medieval Europe and colonial North America. ^[1]

Bacteria can also reduce iron rather than oxidise it. Geobacter metallireducens and Shewanella putrefaciens both oxidise organic material in sediment and reduce Fe³⁺ in ferric hydroxides to Fe²⁺ as part of their metabolic processes. The reduced iron then crystallises as magnetite (Fe₃O₄), forming very small grains outside the cells. These biogenic magnetite grains can contribute to the remanent magnetism preserved in sedimentary rocks. ^[1]

Carbonate Precipitation by Cyanobacteria

Cyanobacteria drive carbonate precipitation by photosynthesis. The reaction is: ^[1]

Photosynthetic fixation of inorganic carbon raises the pH of the water (making it less acidic), which reduces the solubility of calcium carbonate until it becomes oversaturated. The ligands on cyanobacterial surfaces attract and hold Ca²⁺, promoting heterogeneous nucleation of calcite or aragonite. In environments where other divalent cations are available, the carbonate product may instead be dolomite [CaMg(CO₃)₂], strontianite (SrCO₃), or magnesite (MgCO₃). Cyanobacterial mats that repeatedly trap and bind carbonate sediment produce stromatolites. ^[1]

Biologically Controlled Mineralization

Biologically controlled mineralization involves an organism expending cellular energy to concentrate specific elements and precipitate minerals that serve a physiological purpose. The organism is not simply a passive nucleation site or an accidental chemist - it is actively building a structure. ^[1] The cation of choice is usually calcium, and the most common products are carbonates and phosphates, though oxides and sulfides are also produced. Organisms most commonly use controlled mineralisation to create skeletal structures. ^[1]

Coccolithophores and Foraminifera

Coccolithophores are unicellular algae that build microscopic plates of calcite called coccoliths, which accumulate as micritic mud in limestone sequences. They have been abundant in the oceans since the Jurassic, and in the Cretaceous experienced a population explosion associated with widespread limestone deposition worldwide. Most species are planktonic, living in the photic zone at mid- to high-latitude coastal settings. ^[1]

Foraminifera are both planktonic and benthic (bottom-dwelling) organisms that secrete shells ranging in size from about 30 μm to more than 1 mm. They first appeared in the Cambrian and occupy a wide range of marine environments. ^[1]

Carbonate Apatite: Bones and Teeth

Carbonate apatite, Ca₅(PO₄,CO₃)₃(OH), is the biomineral of greatest importance to vertebrates. It forms the mineral content of bones and teeth, and also the shells of inarticulate brachiopods. Phosphorus and calcium from dietary sources are combined in bone- and tooth-forming cells to precipitate as small platelets of apatite. ^[1]

Bone is a composite of mineral and cellular material. It consists of 45 to 70 wt% apatite plus approximately 10 wt% water, with the remainder being collagen and other proteins. Tooth enamel, in contrast, consists of almost pure apatite with very little organic content. The mineral content of bone is not static - it is continuously dissolving and reprecipitating, with the entire mineral fraction replaced on a timescale of 5 to 10 years. When calcium and phosphorus are needed elsewhere in the body and dietary supply is insufficient, dissolution of bone apatite is promoted to meet those needs. ^[1]

Magnetic Biominerals

Several magnetic minerals are produced by biologically controlled mineralisation. The chiton, a marine mollusc, produces fine grains of magnetite on its radular teeth - the grinding apparatus used to process algae and other food. The scaly-footed snail, found near hydrothermal vents in the Indian Ocean, precipitates greigite (Fe₃S₄) on its foot, apparently as a form of protective armour. More broadly, magnetite (Fe₃O₄) and maghemite (γFe₂O₃) nanoparticles are found in a wide range of organisms including bacteria, algae, molluscs, insects, and vertebrates. In bacteria and insects these magnetic particles appear to function in orientation and navigation; the human brain also contains very small particles of magnetite and maghemite, though their function - if any - remains unknown. ^[1]

Applications

Biomining

Knowledge of how microorganisms interact with minerals has been translated into the industrial process of biomining. Organisms such as Acidithiobacillus ferrooxidans are introduced into crushed ore or ore concentrates. In heap leaching, bacteria-containing solutions are percolated through heaps of crushed ore; in tank bioleaching, the ore and bacterial solution are combined in large tanks. Through metabolic processes, metals are introduced into the aqueous phase and then extracted. Biomining has been applied successfully to copper, cobalt, nickel, zinc, and uranium extraction, and to the removal of unwanted metals from gold and silver ores. Its advantages over conventional smelting include lower energy consumption, reduced sulfur dioxide emissions, lower operating costs, and the ability to process lower-grade ores that would not be economically viable otherwise. ^[1]

Bioremediation

Bioremediation uses plants and bacteria to remove unwanted chemicals from the environment. For organic contaminants such as crude oil and petroleum products - which adhere to mineral particles in soil and are difficult to remove by physical means - bacteria can metabolise the contaminants directly and remove them both in place and in processing facilities. For metal contamination from mine waste, bacteria and plants extract metals from surface water through precipitation, sorption onto mineral particles, and uptake into plant tissue. ^[1]

Bio-mediation of Soil Engineering

The metabolism of Sporosarcina pasteurii raises pore-water pH in soils, which under appropriate conditions causes calcite (CaCO₃) to precipitate from the pore fluid. This calcite cements soil particles together, reducing permeability and increasing shear strength. This bio-mediation of soil engineering properties is being studied as a method for improving weak soils, at least under laboratory conditions. ^[1]

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