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Marine biogenic calcification is the production of
calcium carbonate Calcium carbonate is a chemical compound with the chemical formula . It is a common substance found in Rock (geology), rocks as the minerals calcite and aragonite, most notably in chalk and limestone, eggshells, gastropod shells, shellfish skel ...
by organisms in the global ocean. Marine biogenic calcification is the biologically mediated process by which marine organisms produce and deposit calcium carbonate minerals to form
skeletal A skeleton is the structural frame that supports the body of most animals. There are several types of skeletons, including the exoskeleton, which is a rigid outer shell that holds up an organism's shape; the endoskeleton, a rigid internal fram ...
structures or hard tissues. This process is a fundamental aspect of the life cycle of some marine organisms, including
corals Corals are colonial marine invertebrates within the subphylum Anthozoa of the phylum Cnidaria. They typically form compact Colony (biology), colonies of many identical individual polyp (zoology), polyps. Coral species include the important Coral ...
,
mollusks Mollusca is a phylum of protostomic invertebrate animals, whose members are known as molluscs or mollusks (). Around 76,000 extant species of molluscs are recognized, making it the second-largest animal phylum after Arthropoda. The num ...
,
foraminifera Foraminifera ( ; Latin for "hole bearers"; informally called "forams") are unicellular organism, single-celled organisms, members of a phylum or class (biology), class of Rhizarian protists characterized by streaming granular Ectoplasm (cell bio ...
, certain types of
plankton Plankton are the diverse collection of organisms that drift in Hydrosphere, water (or atmosphere, air) but are unable to actively propel themselves against ocean current, currents (or wind). The individual organisms constituting plankton are ca ...
, and other calcifying
marine invertebrates Marine invertebrates are invertebrate animals that live in marine habitats, and make up most of the macroscopic life in the oceans. It is a polyphyletic blanket term that contains all marine animals except the marine vertebrates, including the ...
. The resulting structures, such as shells, skeletons, and coral reefs, function as protection, support, and shelter and create some of the most biodiverse habitats in the world. Marine biogenic calcifiers also play a key role in the
biological carbon pump The biological pump (or ocean carbon biological pump or marine biological carbon pump) is the ocean's biologically driven Carbon sequestration, sequestration of carbon from the atmosphere and land runoff to the ocean interior and seafloor sedim ...
and the biogeochemical cycling of nutrients,
alkalinity Alkalinity (from ) is the capacity of water to resist Freshwater acidification, acidification. It should not be confused with base (chemistry), basicity, which is an absolute measurement on the pH scale. Alkalinity is the strength of a buffer s ...
, and organic matter.


Processes of Marine Biogenic Calcification


Biochemical mechanisms


Cellular and molecular processes of biogenic calcification

Calcium carbonate plays a fundamental role in the skeletal formation of marine calcifiers. The skeletal structures of these organisms are predominantly composed of calcium carbonate minerals, specifically
aragonite Aragonite is a carbonate mineral and one of the three most common naturally occurring crystal forms of calcium carbonate (), the others being calcite and vaterite. It is formed by biological and physical processes, including precipitation fr ...
and
calcite Calcite is a Carbonate minerals, carbonate mineral and the most stable Polymorphism (materials science), polymorph of calcium carbonate (CaCO3). It is a very common mineral, particularly as a component of limestone. Calcite defines hardness 3 on ...
. These structures provide support, protection, and housing for marine calcifiers and are formed through the biochemical processes of biomineralization to precipitate the crystal structures that form the hard tissues of these organisms. The biogenic formation of calcium carbonate structures is the result of a combination of biological and physical processes such as genetics, cellular activity, crystal competition, growth in confined spaces, and self-organization processes. The composition of these structures, and the mechanisms involved in building them, are highly diverse. For example, some corals can incorporate both calcite and aragonite polymorphs into their skeletons. Some species, like corals and byrozoans, can incorporate other minerals to form complex protein matrices that perform specific functions. The key steps involved in marine biogenic calcification include the uptake of dissolved calcium ions (Ca2+) and carbonate ions (CO32-) from seawater, the precipitation of calcium carbonate crystals, and the controlled formation of skeletal structures through biomineralization processes. These organisms often regulate the calcification process through the secretion of organic molecules and proteins that influence the
nucleation In thermodynamics, nucleation is the first step in the formation of either a new Phase (matter), thermodynamic phase or Crystal structure, structure via self-assembly or self-organization within a substance or mixture. Nucleation is typically def ...
and growth of crystalline structures. A range of biochemical calcification (biocalcification) mechanisms exist, indicated by the fact that marine calcifiers use different forms of calcium carbonate minerals. Within this range of mechanisms, there are two broad categories of biogenic calcification in marine organisms: extracellular mineralization and intracellular mineralization. In particular, mollusks and corals use the extracellular strategy in which ion exchange pumps actively pump ions out of a cell into the extracellular space, where environmental conditions, such as pH, can be tightly controlled. In contrast, during intracellular mineralization the calcium carbonate is formed within the organism and can either be kept within the organism as an internal structure or is later moved to the outside while retaining the
cell membrane The cell membrane (also known as the plasma membrane or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane that separates and protects the interior of a cell from the outside environment (the extr ...
covering. Broadly, the intracellular mechanism pumps ions into a vesicle within the cell. This vesicle can then be secreted to the outside of the organism. Often, cells will fuse their membranes and combine these vesicles in order to build very large calcium carbonate structures that would not be possible within a single cell.


Forms of calcium carbonate

The three most common calcium carbonate minerals are
aragonite Aragonite is a carbonate mineral and one of the three most common naturally occurring crystal forms of calcium carbonate (), the others being calcite and vaterite. It is formed by biological and physical processes, including precipitation fr ...
,
calcite Calcite is a Carbonate minerals, carbonate mineral and the most stable Polymorphism (materials science), polymorph of calcium carbonate (CaCO3). It is a very common mineral, particularly as a component of limestone. Calcite defines hardness 3 on ...
, and
vaterite Vaterite is a mineral, a polymorphism (materials science), polymorph of calcium carbonate (calcium, Cacarbon, Coxygen, O3). It was named after the German mineralogist Heinrich Vater. It is also known as mu-calcium carbonate (μ-CaCO3). Vaterite b ...
. Although these minerals have the same chemical formula (CaCO3), they are considered polymorphs because the atoms that make up the molecule are stacked in different arrangements. For example, aragonite minerals have an
orthorhombic crystal In crystallography, the orthorhombic crystal system is one of the 7 crystal systems. Orthorhombic Lattice (group), lattices result from stretching a cubic crystal system, cubic lattice along two of its orthogonal pairs by two different factors, res ...
lattice structure, while calcite crystals have a
trigonal In crystallography, the hexagonal crystal family is one of the six crystal family, crystal families, which includes two crystal systems (hexagonal and trigonal) and two lattice systems (hexagonal and rhombohedral). While commonly confused, the tr ...
structure. Some of the calcite polymorphs are further subdivided by relative magnesium content (Mg/Ca ratio), with calcite
solubility In chemistry, solubility is the ability of a chemical substance, substance, the solute, to form a solution (chemistry), solution with another substance, the solvent. Insolubility is the opposite property, the inability of the solute to form su ...
increasing with increasing Mg. The solubility of various forms of CaCO3 differs in seawater; specifically, aragonite exhibits greater solubility compared to pure calcite.


Chemical processes and saturation state

The surface ocean engages in air-sea interactions and absorbs
carbon dioxide Carbon dioxide is a chemical compound with the chemical formula . It is made up of molecules that each have one carbon atom covalent bond, covalently double bonded to two oxygen atoms. It is found in a gas state at room temperature and at norma ...
(CO2) from the atmosphere, making the ocean the Earth's largest sink for atmospheric CO2. Carbon dioxide dissolves in and reacts with seawater to form
carbonic acid Carbonic acid is a chemical compound with the chemical formula . The molecule rapidly converts to water and carbon dioxide in the presence of water. However, in the absence of water, it is quite stable at room temperature. The interconversion ...
. Subsequent reactions then produce
carbonate A carbonate is a salt of carbonic acid, (), characterized by the presence of the carbonate ion, a polyatomic ion with the formula . The word "carbonate" may also refer to a carbonate ester, an organic compound containing the carbonate group ...
(CO32−),
bicarbonate In inorganic chemistry, bicarbonate (IUPAC-recommended nomenclature: hydrogencarbonate) is an intermediate form in the deprotonation of carbonic acid. It is a polyatomic anion with the chemical formula . Bicarbonate serves a crucial bioche ...
(HCO3), and hydrogen (H+) ions. Carbonate and bicarbonate are also deposited into the global ocean by rivers through the weathering of rock formations. The three species of carbon in seawater, carbon dioxide, bicarbonate, and carbonate, make up the total concentration of dissolved organic carbon (DIC) in the ocean. Approximately 90% of DIC is bicarbonate ions, 10% is carbonate ions, and <1% is dissolved carbon dioxide, with some spatial variation. The equilibria reactions between these species result in the buffering of seawater in terms of the concentrations of hydrogen ions present.Dickson, Andrew. (2010). The carbon dioxide system in seawater: Equilibrium chemistry and measurements. Guide to Best Practices for Ocean Acidification Research and Data Reporting. 17-40. The following chemical reactions exhibit the dissolution of carbon dioxide in seawater and its subsequent reaction with water: CO2(g) + H2O(l) ⥨ H2CO3(aq) H2CO3(aq) ⥨ HCO3(aq) + H+(aq) HCO3(aq) ⥨ CO32−(aq) + H+(aq) This series of reactions governs the pH levels in the ocean and also dictates the saturation state of seawater, indicating how saturated or unsaturated the seawater is with
carbonate A carbonate is a salt of carbonic acid, (), characterized by the presence of the carbonate ion, a polyatomic ion with the formula . The word "carbonate" may also refer to a carbonate ester, an organic compound containing the carbonate group ...
ions. Consequently, the saturation state significantly influences the balance between the dissolution and calcification processes in marine biogenic calcifiers. When seawater is oversaturated with calcium carbonate, the concentration of calcium ions and carbonate ions exceed the saturation point for a particular mineral, such as
aragonite Aragonite is a carbonate mineral and one of the three most common naturally occurring crystal forms of calcium carbonate (), the others being calcite and vaterite. It is formed by biological and physical processes, including precipitation fr ...
or
calcite Calcite is a Carbonate minerals, carbonate mineral and the most stable Polymorphism (materials science), polymorph of calcium carbonate (CaCO3). It is a very common mineral, particularly as a component of limestone. Calcite defines hardness 3 on ...
, which make up the skeletons of many marine organisms. Such conditions are favorable to marine calcifiers for the formation of calcium carbonate skeletons or shells. When seawater is undersaturated, meaning the concentration of calcium and carbonate ions is below the saturation point, it becomes challenging for marine calcifiers to build and maintain their skeletal structures, as the
equilibrium Equilibrium may refer to: Film and television * ''Equilibrium'' (film), a 2002 science fiction film * '' The Story of Three Loves'', also known as ''Equilibrium'', a 1953 romantic anthology film * "Equilibrium" (''seaQuest 2032'') * ''Equilibr ...
conditions favor dissolution of calcium carbonate. As a general rule, seawater that is undersaturated (Ω < 1) can dissolve the structures of calcifying organisms. However, many organisms see negative effects on growth at saturation states above Ω = 1. For example, a saturation state of  Ω = 3 is optimal for coral growth, so a saturation state Ω < 3 can potentially have negative effects on coral growth and survival. Calcium carbonate saturation can be determined using the following equation: Ω = ( a2+CO32−])/Ksp where the numerator ( a2+CO32−]) denotes the concentration of calcium and carbonate ions and the denominator (Ksp) refers to the mineral (solid) phase stoichiometric solubility product of calcium carbonate. When saturation is high, organisms can extract calcium and carbonate ions from seawater, forming solid crystals of calcium carbonate: Ca2+(aq) + 2HCO3(aq) → CaCO3(s) + CO2 + H2O For marine calcifiers to build and maintain calcium carbonate structures, CaCO3 production must be greater than CaCO3 loss through physical, chemical, and biological processes. This net production can be thought of as follows: CaCO3 accretion = CaCO3 production – CaCO3 dissolution – physical loss of CaCO3 The decreasing saturation of seawater with respect to calcium carbonate, associated with
ocean acidification Ocean acidification is the ongoing decrease in the pH of the Earth's ocean. Between 1950 and 2020, the average pH of the ocean surface fell from approximately 8.15 to 8.05. Carbon dioxide emissions from human activities are the primary cause of ...
, a result of increased carbon dioxide (CO2) absorption by the oceans, poses a significant threat to marine calcifiers. As CO2 concentrations in seawater rise, a decrease in pH and a reduction in carbonate ion concentrations in seawater follows. And, since calcification is a source of CO2 to the surrounding water, decreased rates of global calcification would inversely affect the rate of atmospheric CO2 absorption, perpetuating these effects. This can make it difficult for marine organisms to
precipitate In an aqueous solution, precipitation is the "sedimentation of a solid material (a precipitate) from a liquid solution". The solid formed is called the precipitate. In case of an inorganic chemical reaction leading to precipitation, the chemic ...
and maintain their calcium carbonate structures, affecting growth, development, and overall health. The widespread use of calcification by marine organisms has relied on the ability of calcium carbonate to readily form in seawater, where the saturation states (Ω) of aragonite and calcite minerals have consistently surpassed Ω = 1 (indicating oversaturation) in surface waters for hundreds of millions of years. The impacts of reduced calcium carbonate saturation on marine calcifiers have broader ecological implications, as these organisms play vital roles in marine ecosystems. For example, coral reefs, which are built by coral polyps secreting calcium carbonate skeletons, are particularly vulnerable to changes in calcium carbonate saturation. There is much debate in the scientific community on whether calcification rates correlate more with carbonate ions and saturation state or with pH. Some researchers state that a correlation exists between calcification and the Ω of carbonate ions in seawater. Meanwhile, others state that from a physiological standpoint there are numerous marine organisms, and their calcification control is attributed more so to the concentrations of seawater bicarbonate (HCO3−) and protons (H+) rather than the Ω. Further research is essential to gain a comprehensive understanding of the intricate connections between Ω, ocean acidification, and their impacts on the calcification rates of marine biogenic calcifiers, elucidating the distinct roles played by each.


Marine Calcifying Organisms


Corals

Coral reefs, physical structures formed from calcium carbonate, are important on biological and ecological scales to the regions they are endemic to. Their robust calcification abilities have resulted in extensive calcium carbonate deposits, some housing significant hydrocarbon reserves. However, this group only accounts for about 10% of the global production of calcium carbonate. Corals undergo extracellular calcification and first develop an organic matrix and skeleton on top of which they will form their calcite structures. It is proposed that calcification via pH upregulation of the coral's extracellular calcifying fluid occurs at least in part via Ca2+-ATPase. Ca2+-ATPase is an enzyme in the calicoblastic epithelium that pumps Ca2+ ions into the calcifying region and ejects protons (H+). This process circumvents the kinetic barriers to CaCO3precipitation that exist naturally in seawater.


Molluscs

Mollusks are a diverse group including slugs,
oyster Oyster is the common name for a number of different families of salt-water bivalve molluscs that live in marine or brackish habitats. In some species, the valves are highly calcified, and many are somewhat irregular in shape. Many, but no ...
s,
limpet Limpets are a group of aquatic snails with a conical gastropod shell, shell shape (patelliform) and a strong, muscular foot. This general category of conical shell is known as "patelliform" (dish-shaped). Existing within the class Gastropoda, ...
s,
snail A snail is a shelled gastropod. The name is most often applied to land snails, terrestrial molluscs, terrestrial pulmonate gastropod molluscs. However, the common name ''snail'' is also used for most of the members of the molluscan class Gas ...
s,
scallop Scallop () is a common name that encompasses various species of marine bivalve molluscs in the taxonomic family Pectinidae, the scallops. However, the common name "scallop" is also sometimes applied to species in other closely related famili ...
s,
mussel Mussel () is the common name used for members of several families of bivalve molluscs, from saltwater and Freshwater bivalve, freshwater habitats. These groups have in common a shell whose outline is elongated and asymmetrical compared with other ...
s,
clam Clam is a common name for several kinds of bivalve mollusc. The word is often applied only to those that are deemed edible and live as infauna, spending most of their lives halfway buried in the sand of the sea floor or riverbeds. Clams h ...
s,
cephalopod A cephalopod is any member of the molluscan Taxonomic rank, class Cephalopoda (Greek language, Greek plural , ; "head-feet") such as a squid, octopus, cuttlefish, or nautilus. These exclusively marine animals are characterized by bilateral symm ...
s and others. Mollusks employ a strategic approach to protect their soft tissues and deter predation by developing an external calcified shell. This process involves specialized cells following genetic instructions to synthesize minerals under non-equilibrium conditions. The resulting minerals exhibit complex shapes and sizes along with being formed within a confined space. These organisms also pump hydrogen out of the calcifying area so that it will not bond to the carbonate ions, which prevents crystallization of calcium carbonate.


Echinoderms

Echinoderms, of the phylum Echinodermata, include organisms such as sea stars, sea urchins, sand dollars, crinoids, sea cucumbers and brittle stars. These organisms form extensive  endoskeletons consisting of magnesium-rich calcite. Magnesium-rich calcite maintains the chemical composition of CaCO3, yet features substitutions of Mg for Ca as calcite and aragonite are mineral forms or polymorphs of CaCO3. Adult echinoderm skeletons consist of teeth, spines, tests, tubule feet, and in some cases, spicules. Echinoderms serve as excellent blueprints for biomineralization. Adult sea urchins are a particularly popular species studied to better understand the molecular and cellular processes that the calcification and biomineralization of their skeletal structures requires. Unlike many other marine calcifiers, echinoderm tests are not formed purely from calcite; instead, their structures also heavily consist of organic matrices that increases the toughness and strength of their endoskeletons.


Crustaceans

Crustacean Crustaceans (from Latin meaning: "those with shells" or "crusted ones") are invertebrate animals that constitute one group of arthropods that are traditionally a part of the subphylum Crustacea (), a large, diverse group of mainly aquatic arthrop ...
s have a hard outer shell formed from calcium carbonate. These organisms form a network of chitin-protein fibers and then precipitate calcium carbonate within this matrix. The
chitin Chitin (carbon, C8hydrogen, H13oxygen, O5nitrogen, N)n ( ) is a long-chain polymer of N-Acetylglucosamine, ''N''-acetylglucosamine, an amide derivative of glucose. Chitin is the second most abundant polysaccharide in nature (behind only cell ...
-protein fibers are first hardened by
sclerotization Sclerotization is a biochemical process that produces the rigid shell of sclerotin that comprises an insect's chitinous exoskeleton. It is prominent in the thicker, armored parts of insects and arachnid Arachnids are arthropods in the Class (b ...
, or crosslinking of protein and
polysaccharide Polysaccharides (), or polycarbohydrates, are the most abundant carbohydrates found in food. They are long-chain polymeric carbohydrates composed of monosaccharide units bound together by glycosidic linkages. This carbohydrate can react with wat ...
s, followed by the crosslinking of proteins with other proteins. The presence of a hard, calcified exoskeleton means that the crustacean has to
molt In biology, moulting (British English), or molting (American English), also known as sloughing, shedding, or in many invertebrates, ecdysis, is a process by which an animal casts off parts of its body to serve some beneficial purpose, either at ...
and shed the exoskeleton as its body size increases. This links molting cycles to calcification processes, making access to a regular source of calcium and carbonate ions crucial for the growth and survival of crustaceans. Various body parts of the crustacean will have a different mineral content, varying the hardness at these locations with the harder areas being generally stronger. This calcite shell provides protection for the crustaceans, meaning between molting cycles the crustacean must avoid predators while it waits for its calcite shell to form and harden.


Foraminifera

Foraminifera Foraminifera ( ; Latin for "hole bearers"; informally called "forams") are unicellular organism, single-celled organisms, members of a phylum or class (biology), class of Rhizarian protists characterized by streaming granular Ectoplasm (cell bio ...
, or forams, are single-celled protists that form chambered shells (tests) from calcium carbonate. Forams first appeared approximately 170 million years ago, and populate oceans globally. Forams are microscopic organisms, typically no larger than 1 mm in length.  The calcification and dissolution of their shells causes changes both in the surface seawater carbonate chemistry, and in deep-water chemistry. These organisms are excellent paleo-proxies as they record ambient water chemistry during shell formation and are well-preserved in the sedimentary fossil record. Planktonic foraminifera, found in large numbers in the ocean, contribute significantly to oceanic carbonate production. Unlike their benthic counterparts, more of these species have algal symbionts.


Coccolithophores

Phytoplankton Phytoplankton () are the autotrophic (self-feeding) components of the plankton community and a key part of ocean and freshwater Aquatic ecosystem, ecosystems. The name comes from the Greek language, Greek words (), meaning 'plant', and (), mea ...
, especially haptophytes such as
coccolithophores Coccolithophores, or coccolithophorids, are single-celled organisms which are part of the phytoplankton, the autotrophic (self-feeding) component of the plankton community. They form a group of about 200 species, and belong either to the kingd ...
, are also well known for their calcium carbonate production. It is estimated that these phytoplankton may contribute up to 70% of the global calcium carbonate precipitation, and coccolithophores are the largest phytoplankton contributors, along with diatoms and dinoflagellates. Contributing between 1 and 10% of total ocean primary productivity, 200 species of coccolithophores live in the ocean, and under the right conditions they can form large blooms. These large bloom formations are a driving force for the export of calcium carbonate from the surface to the deep ocean in what is sometimes called “Coccolith rain”. As the coccolithophores sink to the seafloor they contribute to the vertical carbon dioxide gradient in the water column.


Great Calcite Belt of the Southern Ocean

Coccolithophores produce calcite plates termed coccoliths which together cover the entire cell surface forming the coccosphere. The coccoliths are formed using the intracellular strategy where the plates are formed in a coccoliths vesicle, but the product forming within the vesicle varies between the
haploid Ploidy () is the number of complete sets of chromosomes in a cell (biology), cell, and hence the number of possible alleles for Autosome, autosomal and Pseudoautosomal region, pseudoautosomal genes. Here ''sets of chromosomes'' refers to the num ...
and
diploid Ploidy () is the number of complete sets of chromosomes in a cell, and hence the number of possible alleles for autosomal and pseudoautosomal genes. Here ''sets of chromosomes'' refers to the number of maternal and paternal chromosome copies, ...
phases. A coccolithophore in the haploid phase will produce what is called a holococcolith, while one in the diploid phase will produce heterococcoliths. Holococcoliths are small calcite crystals held together in an organic matrix, while heterococcoliths are arrays are larger, more complex calcite crystals. These are often formed over a pre-existing template, giving each plate its particular structure and forming complex designs.  Each coccolithophore is a cell surrounded by the
exoskeleton An exoskeleton () . is a skeleton that is on the exterior of an animal in the form of hardened integument, which both supports the body's shape and protects the internal organs, in contrast to an internal endoskeleton (e.g. human skeleton, that ...
coccosphere, but there exists a wide range of sizes, shapes and architectures between different cells. Advantages of these plates may include protection against infection by viruses and bacteria, as well as protection from grazing
zooplankton Zooplankton are the heterotrophic component of the planktonic community (the " zoo-" prefix comes from ), having to consume other organisms to thrive. Plankton are aquatic organisms that are unable to swim effectively against currents. Consequent ...
. The calcium carbonate exoskeleton enhances the amount of light the coccolithophore can uptake, increasing the level of photosynthesis. Finally, the coccoliths protect the phytoplankton from photodamage by UV light from the sun. The coccolithophores are also important in the geological history of Earth. The oldest coccolithophore fossil records are more than 209 million years old, placing their earliest presence in the Late
Triassic period The Triassic ( ; sometimes symbolized 🝈) is a geologic period and system which spans 50.5 million years from the end of the Permian Period 251.902 million years ago ( Mya), to the beginning of the Jurassic Period 201.4 Mya. The Triassic is the ...
. Their calcium carbonate formation may have been the first deposition of carbonate on the seafloor.


Corallinales (red algae)

Calcifying
rhodophytes Red algae, or Rhodophyta (, ; ), make up one of the oldest groups of eukaryotic algae. The Rhodophyta comprises one of the largest Phylum, phyla of algae, containing over 7,000 recognized species within over 900 Genus, genera amidst ongoing taxon ...
stock their filamentous cell walls with calcium carbonate and magnesium. '' Corallinales'' is the one genus of red algae exists but their distribution ranges across the world's oceans. Examples include ''Corallina'', ''Neogoniolithon'', and ''Harveylithon.'' The magnesium-rich calcium carbonate of ''Corallinales'' cell wall provides shelter from predators and structural integrity in the intertidal zone. The CaCO3 production in Coralline also plays a role in habitat formation and provides resources for benthic invertebrates.


Calcifying bacteria

Evidence shows that some calcifying
cyanobacteria Cyanobacteria ( ) are a group of autotrophic gram-negative bacteria that can obtain biological energy via oxygenic photosynthesis. The name "cyanobacteria" () refers to their bluish green (cyan) color, which forms the basis of cyanobacteri ...
strains have existed for millions of years and contributed to large land formations. About 70 strains of cyanobacteria can precipitate calcium carbonate, including some strains of '' Synechococcus'', ''
Bacillus sphaericus ''Lysinibacillus sphaericus'' (previously known as ''Bacillus sphaericus'') is a Gram-positive, mesophilic, rod-shaped bacterium commonly found on soil. It can form resistant endospores that are tolerant to high temperatures, chemicals and ultrav ...
'', ''Bactilus subtilus'',and ''Sporosarcina psychrophile.''


Morphological variations in calcium carbonate skeletons


Structural adaptations in different marine organisms

Diverse algae exhibit distinct mechanisms of CaCO3 formation, with calcification occurring internally or externally. Calcification may play a role in producing CO2 or supporting processes that need H+, based on the observed partial reaction. Phytoplankton species relying on CO2 diffusion for photosynthesis may face limitations due to CO2 concentration and diffusion to the chloroplast's
Rubisco Ribulose-1,5-bisphosphate carboxylase/oxygenase, commonly known by the abbreviations RuBisCo, rubisco, RuBPCase, or RuBPco, is an enzyme () involved in the light-independent (or "dark") part of photosynthesis, including the carbon fixation by wh ...
site. Calcifying macroalgae like
Halimeda ''Halimeda'' is a genus of green macroalgae. The algal body (thallus) is composed of calcified green segments. Calcium carbonate is deposited in its tissues, making it inedible to most herbivores. However one species, ''Halimeda tuna'', was desc ...
and Corallina also produce CaCO3 in alkaline extracellular spaces. Coccolithophorid phytoplankton form CaCO3 in crystalline structures known as coccoliths, with holococcoliths formed externally and heterococcoliths produced intracellularly. Various coccolithophores produce two coccolith types: Heterococcoliths, from diploid cells, are complex, while holococcoliths, from haploid stages, are less studied. Factors influencing life cycle phase transitions and the role of specific proteins like GPA in coccolith morphology are explored. Polysaccharides, particularly coccolith-associated polysaccharides (CAPs), emerge as key regulators of calcite growth and morphology. CAPs' diverse roles, including nucleation promotion and inhibition, vary between species. External polysaccharides also influence coccolith adhesion and organization. Recent findings link cellular transport processes, carbonate saturation conditions, and regulatory processes determining calcite precipitation rate and morphology. Unexpectedly, silicon's role in coccolith morphology regulation is species-dependent, highlighting physiological distinctions among coccolithophore groups. These revelations raise questions about ecological implications, evolutionary adaptations, and the impact of changing ocean silicate levels on coccolithogenesis. Calcification rates in coccolithophores often correlate with photosynthesis, implying a potential metabolic role. Heterococcoliths develop inside intracellular vesicles, with coccolith formation showing a unity ratio with photosynthetic carbon fixation under high calcification rates. The variability in
isotope fractionation Isotope fractionation describes fractionation processes that affect the relative abundance of isotopes, a phenomena that occurs (and so advantage is taken of it) in the study geochemistry, biochemistry, food science, and other fields. Normally, ...
and calcification mechanisms underscores these organisms' adaptability and complexity in responding to environmental factors. For corals, DIC from the seawater is absorbed and transferred to the coral skeleton. An anion exchanger will then be used to secrete DIC at the site of calcification. This DIC pool is also used by algal symbionts (dinoflagellates) that live in the coral tissue. These algae photosynthesize and produce nutrients, some of which are passed to the coral. The coral in turn will emit ammonium waste products which the algae uptake as nutrients. There has been an observed tenfold increase in calcium carbonate formation in corals containing algal symbionts compared with corals that do not have this symbiotic relationship. The coral algal symbionts, Symbiodinium, show decreased populations with increased temperatures, often leaving the coral colorless and unable to photosynthesize and losing pigments (known as coral bleaching).


Evolution of biogenic calcification

The evolution of biogenic calcification and carbonate structures within the eukaryotic domain is complex, highlighted by the distribution of mineralized skeletons across major clades. Five out of the eight major clades feature species with mineralized skeletons, and all five clades involve organisms that precipitate calcite or aragonite. Skeletal evolution occurred independently in foraminiferans and echinoderms, suggesting two separate origins of CaCO3 skeletons. The
common ancestry Common descent is a concept in evolutionary biology applicable when one species is the ancestor of two or more species later in time. According to modern evolutionary biology, all living beings could be descendants of a unique ancestor commonl ...
for echinoderm and ascidian skeletons is less clear, but a conservative estimate indicates that carbonate skeletons evolved at least twenty-eight times within Eukarya. Phylogenetic insights highlight repeated innovations in carbonate skeleton evolution, raising questions about homology in underlying molecular processes. Skeleton formation involves controlled mineral precipitation in specific biological environments, requiring directed calcium and carbonate transport, molecular templates, and growth inhibitors. Biochemical similarities, including the synthesis of acidic proteins and glycoproteins guiding mineralization, suggest an ancient capacity for carbonate formation in eukaryotes. While skeletons may not share structural homology, underlying physiological pathways are common, reflecting multiple cooptations of molecular and physiological processes across eukaryotic organisms. The
Cambrian Period The Cambrian ( ) is the first geological period of the Paleozoic Era, and the Phanerozoic Eon. The Cambrian lasted 51.95 million years from the end of the preceding Ediacaran period 538.8 Ma (million years ago) to the beginning of the Ordovici ...
marks a significant watershed in skeletal evolution, with the appearance of mineralized skeletons in various groups.Cloud PE (1968) Pre-metazoan evolution and the origins of the Metazoa. In: Evolution and Environment. Drake T (ed) Yale University Press, New Haven, p 1–72 Skeletal diversity increased during this period, driven by predation pressure favoring protective armor evolution. The Cambrian radiation of mineralized skeletons was likely part of a broader animal diversity expansion. The evolution of mineralized skeletons during the Cambrian did not occur instantly, with a gradual increase in abundance and diversity over 25 million years.Lowenstam HA, Weiner S (1989) On Biomineraliztion. Oxford University Press, Oxford Environmental changes and predation pressure played key roles in shaping skeletal evolution. The diversity of minerals and skeletal architectures during this period challenges explanations solely based on changing ocean chemistry. The interplay between genetic possibility and environmental opportunity, influenced by factors like increased oxygen tensions, likely contributed to Cambrian diversification. Later Cambrian oceans witnessed a decline in mineralized skeletons, potentially influenced by high temperatures and pCO2 associated with a super greenhouse. Skeletal physiological responses to environmental conditions remain an area of study. Large-scale variations in carbonate chemistry suggest a connection between ocean chemistry and the mineralogy of carbonate precipitation. Skeletal organisms that precipitate massive skeletons under limited physiological control show stratigraphic patterns corresponding to shifts in seawater chemistry. This interplay between physiology, evolution, and environment underscores the complexity of mineralized skeleton evolution across geological time.


Calcium carbonate cycling and the biological carbon pump

The calcium carbonate cycle in the global ocean is of great significance to the biological, chemical, and physical state of the ocean. Mineral calcium carbonate most commonly presents as calcite in the ocean, and the majority of calcite is produced biologically in the upper layer of the ocean. CaCO3 material is exported from the upper ocean to sediments on the ocean floor where it either dissolves or is buried.Sarmiento, J.; Gruber, N. (2006). ''Ocean Biogeochemical Dynamics''. Princeton University: Princeton University Press. Alternatively, CaCO3 can dissolve or be remineralized within the water column prior to reaching the seafloor. Upon reaching the seafloor, CaCO3 undergoes a diagenetic process that ends in either dissolution or burial. The distribution of sediments consisting of calcium carbonate is fairly even across the global oceans, but specific locations are determined by the solubility and saturation level of calcium carbonate. The “
biological carbon pump The biological pump (or ocean carbon biological pump or marine biological carbon pump) is the ocean's biologically driven Carbon sequestration, sequestration of carbon from the atmosphere and land runoff to the ocean interior and seafloor sedim ...
” is a colloquial term coined by scientists to summarize the global carbon cycle in the ocean and its relationship to the biological processes that occur throughout the ocean. The calcium carbonate cycle is inherently linked to the biological pump. The formation of biogenic calcium carbonate by marine calcifiers is one way to add ballast to sinking particles and enhance transport of carbon to the deep ocean and seafloor. The calcium carbonate counter pump refers to the biological process of precipitation of carbonate and the sinking of particulate inorganic carbon. This process releases CO2 into the surface ocean and atmosphere across timescales spanning 100 to 1,000 years. Its crucial role in regulating atmospheric pCO2 significantly influences global changes in atmospheric CO2 concentration.


Inorganic sources of calcium carbonate

Of all the metals important to biogeochemical cycles in the ocean,
calcium Calcium is a chemical element; it has symbol Ca and atomic number 20. As an alkaline earth metal, calcium is a reactive metal that forms a dark oxide-nitride layer when exposed to air. Its physical and chemical properties are most similar to it ...
is one of the most significant in both its mobility and the role it plays in regulating climate over millions of years through its presence in calcium carbonate. Calcium has the ability to migrate relatively easily between the
hydrosphere The hydrosphere () is the combined mass of water found on, under, and above the Planetary surface, surface of a planet, minor planet, or natural satellite. Although Earth's hydrosphere has been around for about 4 billion years, it continues to ch ...
, the
biosphere The biosphere (), also called the ecosphere (), is the worldwide sum of all ecosystems. It can also be termed the zone of life on the Earth. The biosphere (which is technically a spherical shell) is virtually a closed system with regard to mat ...
, and the crust of the Earth. Calcium and
bicarbonate In inorganic chemistry, bicarbonate (IUPAC-recommended nomenclature: hydrogencarbonate) is an intermediate form in the deprotonation of carbonic acid. It is a polyatomic anion with the chemical formula . Bicarbonate serves a crucial bioche ...
ions are largely deposited into the ocean from the
weathering Weathering is the deterioration of rocks, soils and minerals (as well as wood and artificial materials) through contact with water, atmospheric gases, sunlight, and biological organisms. It occurs '' in situ'' (on-site, with little or no move ...
of rock formations and are transported via riverine input. This process occurs on very long timescales. Weathering accounts for approximately 60-90% of solute calcium within the global calcium cycle.
Limestone Limestone is a type of carbonate rock, carbonate sedimentary rock which is the main source of the material Lime (material), lime. It is composed mostly of the minerals calcite and aragonite, which are different Polymorphism (materials science) ...
rock, which consists mostly of calcite, is a prime example of a rich source of calcium to the ocean. The source of the majority of inorganic calcium present in the ocean is due to riverine deposition, though volcanic activity interacting with seawater does provide some calcium as well. The distribution of calcium sources described above is the case for both the present day oceanic calcium budget, and the historical budget over the last 25 million years. The formation of biogenic calcium carbonate is the primary mechanism of removal of calcium in the ocean
water column The (oceanic) water column is a concept used in oceanography to describe the physical (temperature, salinity, light penetration) and chemical ( pH, dissolved oxygen, nutrient salts) characteristics of seawater at different depths for a defined ...
.


Impact of environmental factors on calcification


Rising temperature and light exposure

Marine biogenic calcifiers, such as corals, are facing challenges due to increasing ocean temperatures, leading to prolonged warming events. When sea surface temperatures exceed the local summer maximum monthly mean, coral bleaching and mortality occur as a result of the breakdown in symbiosis with Symbiodiniaceae. Predicted increases in summer-time temperatures, coupled with
ocean warming Ocean heat content (OHC) or ocean heat uptake (OHU) is the energy absorbed and stored by oceans, and is thus an important indicator of Climate change, global warming. Ocean heat content is calculated by measuring ocean temperature at many differe ...
, are expected to impact coral health and overall rates of calcification, particularly in tropical regions where many corals already live close to their upper thermal limits. Corals are highly adapted to their local seasonal temperature and light conditions, influencing their physiology and calcification rates. While increased temperature or light levels typically stimulate calcification up to a certain optimum, beyond which rates decline, the effects of temperature and light on the calcifying fluid chemistry are less clear. Coral calcification is a biologically mediated process influenced by the regulation of internal calcifying fluid chemistry, including pH and dissolved inorganic carbon. The impacts of temperature and light on these factors remain a knowledge gap, with laboratory studies yielding contrasting results. Decoupling the effects of temperature and light on calcification processes is challenging due to their seasonal co-variation, highlighting the need for further research to address this gap and enhance our understanding of how marine biogenic calcifiers respond to future climate change.


Ocean Acidification

Calcifying organisms are particularly at risk due to changes in the chemical composition of ocean water associated with ocean acidification. As pH decreases due to ocean acidification, the availability of carbonate ions (CO32-) in seawater also decreases. Therefore, calcifying organisms experience difficulty building and maintaining their skeletons or shells in an acidic environment. There has been considerable debate in the literature regarding whether organisms are responding to reduced pH or reduced mineral saturation state as both variables decline with ocean acidification. However, recent studies that have isolated the effects of saturation state independent of pH changes point toward saturation state as the most important factor impacting shell formation development. However, we still need to fully constrain the carbonate chemistry to better interpret the ecological responses around ocean acidification. Responses of marine calcifiers to reduced carbonate ion availability are seen in different ways. For example, coral reefs experience inhibited growth at decreased pH, and live calcium carbonate structures experience weakening of existing structures. Other organisms are particularly vulnerable in the early stages of their life cycle.
Bivalves Bivalvia () or bivalves, in previous centuries referred to as the Lamellibranchiata and Pelecypoda, is a class of aquatic molluscs (marine and freshwater) that have laterally compressed soft bodies enclosed by a calcified exoskeleton consis ...
for instance are particularly susceptible during early larval stages during initial shell formation since these early stages have a high energetic cost to the individual's development. In contrast, adult bivalves are considerably more resilient to reduced pH.


Human interactions and applications


Economic importance


Shellfish industry

Ocean acidification (OA) presents a formidable threat to global shellfish production, particularly exerting its impact on calcification processes. Projections indicate that by the end of the century, mussel and oyster calcification could witness substantial reductions of 25% and 10%, respectively, as outlined in the IPCC IS92a scenario, which has an emissions trajectory that results in atmospheric CO2 reaching approximately 740 ppm in 2100. These species, integral to coastal ecosystems and representing a significant portion of global aquaculture, play crucial roles as ecosystem engineers. The anticipated decline in calcification due to OA not only jeopardizes coastal biodiversity and ecosystem functioning but also carries the potential for considerable economic losses. For example, global aquaculture production for shellfish contributed US$29.2 billion to the world economy. Damaged shell surfaces, primarily resulting from reduced calcification rates, contribute to a significant decrease in sale prices, marking a critical economic concern. Economic assessments reveal that such damages, particularly impacting culture quasi-profits or applied cultural value, can lead to reductions ranging from 35% to 70%. Furthermore, when accounting for assumed pH-driven changes occurring concurrently, quasi-profits diminish even more substantially, reaching levels of 49% to 84% across diverse OA scenarios. Consequently, the economic fallout is substantial, with the UK facing potential direct losses of £3 to £6 billion in GDP by 2100, and globally, costs exceeding US$100 billion. These findings emphasize the urgent need for proactive measures to mitigate OA's impact on bivalve farming and underscore the importance of comprehensive climate policies to address these multifaceted challenges.


Coral reef tourism

For organisms relying on calcified structures (e.g. such as reef-associated organisms), OA can potentially disrupt entire ecosystems. As calcifiers play crucial roles in maintaining marine biodiversity, the repercussions of coral reef decline extend beyond economic considerations, emphasizing the urgency of comprehensive conservation efforts. Extensive degradation is occurring in the Caribbean and Western Atlantic region's coral reefs, stemming from issues like disease, overfishing, and a range of human activities. Adding to the challenges, rapid climate-induced ocean warming and acidification exacerbate the threats to these vital ecosystems. Tourism is integral to the Caribbean region with the sector contributing to over 15 percent of GDP and sustaining 13 percent of jobs in the region as a whole. In the face of these challenges, the worldwide combined economic value of coral reefs is an estimated average of US$490 per hectare annually. Specific regions showcase the economic significance of coral reefs, with Hawai'i's contributing US$360 million annually to its economy, and the Philippine economy receiving at least US$1.06 billion each year from coral reefs. In the St. Martin region, coral reefs contribute significantly, emphasizing the need for prioritized conservation and protection efforts. Proposed solutions encompass ecological measures such as water quality management, sustainable fishing practices, ecological engineering, and marine spatial planning. Additionally, socio-economic strategies involve establishing a regional reef secretariat, integrating reef health into blue economy plans, and initiating a reef labeling program to foster corporate partnerships.


See also

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Ocean acidification Ocean acidification is the ongoing decrease in the pH of the Earth's ocean. Between 1950 and 2020, the average pH of the ocean surface fell from approximately 8.15 to 8.05. Carbon dioxide emissions from human activities are the primary cause of ...
- a threat for marine biogenic calcification *
Protist shell Many protists have protective shells or tests, usually made from silica (glass) or calcium carbonate (chalk). Protists are a diverse group of eukaryote organisms that are not plants, animals, or fungi. They are typically microscopic unicellula ...
*
Seashell A seashell or sea shell, also known simply as a shell, is a hard, protective outer layer usually created by an animal or organism that lives in the sea. Most seashells are made by Mollusca, mollusks, such as snails, clams, and oysters ...
*
Shell growth in estuaries Shell growth in estuaries is an aspect of marine biology that has attracted a number of scientific research studies. Many groups of marine organisms produce calcified exoskeletons, commonly known as seashell, shells, hard calcium carbonate struct ...


References

{{reflist Biomineralization