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Marine biogenic calcification
Marine Biogenic Calcification refers to the organic production of calcium carbonate by organisms in the global ocean.

Importance and roles in marine ecosystems
''Marine biogenic calcification is the biologically-mediated process by which marine organisms produce and deposit calcium carbonate minerals to form skeletal structures or hard tissues. This process is a fundamental aspect of the life cycle of some marine organisms, including corals, mollusks, foraminifera, certain types of plankton, and other calcifying marine invertebrates. The resulting structures, such as shells, skeletons, and coral reefs, serve functions such as protection, support, and housing. Marine biogenic calcifiers also play a key role in the biological carbon pump and the biogeochemical cycling of nutrients, alkalinity, and organic matter.''

Inorganic sources of calcium carbonate
''Of all the metals important to biogeochemical cycles in the ocean, calcium 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 biosphere, and the crust of the Earth.''

''Calcium and bicarbonate ions are largely deposited into the ocean from the weathering 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 (Tipper et al. 2016). Limestone rock, which consists mostly of calcite,  is a prime example of a rich source of calcium to the ocean (Berner & Berner 1996). 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 (Berner & Berner 1996).''

Saturation state
''The ocean serves as the Earth’s largest sink for atmospheric carbon dioxide (CO2), continuously absorbing CO2 from the air. This carbon dioxide dissolves and reacts with seawater to form carbonic acid. Subsequent reactions then produce carbonate (CO32−), bicarbonate (HCO3−), and hydrogen (H+) ions. Carbonate and bicarbonate are also deposited in the oceans by rivers via 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.''

Carbon dioxide dissolves in seawater and reacts with water by the following chemical reactions:

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 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 or calcite, which make up the skeletons of many marine organisms. Such conditions are favorable to marine calcifiers for forming and depositing their calcium carbonate skeletons or shells. Conversely, when seawater is undersaturated, meaning the concentration of calcium and carbonate ions is below the saturation point, it becomes challenging for marine organisms to build and maintain their skeletal structures, as the equilibrium conditions favor dissolution of calcium carbonate. The saturation state of seawater with respect to CaCO3 is a measure of its capacity to erode the shells and skeletons of marine calcifiers. As a general rule, seawater that is undersaturated (Ω < 1) can corrode 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.''

''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, often attributed to ocean acidification resulting from increased carbon dioxide (CO2) absorption by the oceans, poses a significant threat to marine calcifiers. As CO2 concentrations, a decrease in pH and a reduction in carbonate ion concentrations in seawater follows. This can make it difficult for marine organisms to precipitate 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.''

Forms of calcium carbonate
The three most common calcium carbonate minerals are aragonite, calcite, and vaterite. 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 lattice structure, while calcite crystals have a trigonal structure. Some of the calcite polymorphs are further subdivided by relative magnesium content (Mg/Ca ratio), with calcite solubility increasing with increasing Mg.

The solubility of various forms of  CaCO3 differs in seawater; specifically, aragonite exhibits greater solubility compared to pure calcite, and the solubility of calcite rises with its magnesium content.

''The ratio of magnesium to calcium (Mg/Ca) in the composition of seawater has been found to have a significant impact on marine calcifiers. There is evidence suggesting that throughout Earth's history, variations in the Mg/Ca ratio of seawater have influenced which calcifying marine organisms were the major reef-builders and sediment-producers throughout different periods of Earth’s history. When the molar Mg/Ca ratio has been greater than 2, (termed "aragonite seas,"), aragonite and high-Mg calcite secreting organisms dominate, while ratios less than 2 (termed "calcite seas"), favor calcite-secreting organisms.''

''Additionally, laboratory experiments have shown that aragonite-secreting bryopsidalean algae and scleractinian corals, as well as calcite-secreting coccolithophores, demonstrate higher rates of calcification and growth when exposed to experimental seawaters with favorable Mg/Ca ratios for their particular skeletal mineral. These findings support the idea that seawater Mg/Ca played a crucial role in determining which calcifying marine organisms were the primary builders of reefs and producers of sediment throughout Earth's history.''

Seawater Alkalinity
The ocean is a key player in the global carbon cycle. Its ability to store carbon dioxide occurs through the reaction of dissolved CO2 with water, which forms bicarbonate. In simple terms, alkalinity is the excess of bases, or the excess of proton acceptors over donors. Ocean alkalinity, defined in mg/L of CaCO3, is important to understand because it provides us with a quantification of the ability of the ocean to store carbon dioxide. This process can also be referred to as providing buffering capacity against ocean acidification. When calcium carbonate dissolves, it releases one unit of dissolved inorganic carbon, and two units of total alkalinity (TA). This increases the pH, which means it is becoming more basic than acidic. This portion of the calcium carbonate cycle is integral to understanding biogeochemical dynamics in the global ocean.

Biochemical mechanisms

 * 1) Role of calcium carbonate in skeletal formation

Influence of environmental factors (temperature, light,  pH) on calcification  (O
''Increasing temperatures have both direct and indirect effects on marine calcification rates. Focusing solely on the direct effects, elevated temperatures affect the rate of chemical reactions and could lead to increased calcification rates, however, if temperatures go over a threshold, it can become stressful for marine organisms, and impair physiological functions. Coral bleaching is an example of how temperature variations impact calcification.''

Cellular/molecular processes involved
''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 and calcite. These skeletal structures provide support, protection, and housing for marine calcifiers and are formed through biochemical processes of biomineralization to precipitate the crystal structures that form the hard tissues of these organisms.''

''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 and growth of crystalline structures.''

''A range of biochemical calcification ( biocalcification) mechanisms exist, indicated by the fact that marine calcifiers use a range of different forms of calcium carbonate minerals. Within this range of mechanisms,'' there are two main types of biogenic calcification in marine organisms. The extracellular biologically induced mineralization involves deposition of calcium carbonate on the exterior of the organism. In contrast, during intracellular mineralization the calcium carbonate is formed within the organism and can either be kept within the organism in a sort of skeleton or internal structure or is later moved to the outside of the organism but retains the cell membrane covering

Mollusks and corals use the extracellular strategy, which is a basic form of calcification where ions are actively pumped out of a cell or are pumped into a vesicle within a cell and then the vesicle containing the calcium carbonate is secreted to the outside of the organism. However, there are obstacles to overcome. The saturation state must be high enough for calcification, and the organism must control the hydrogen ion concentration in the surrounding area. Hydrogen interferes with shell formation because it can bond with carbonate ions. This would reduce the amount of carbonate available to the organism for shell building. To counteract this effect, the organism can pump hydrogen out, thereby increasing the amount of free carbonate ions for calcification.

Overview of Marine Biogenic Calcifiers

 * 1) Morphological variations in calcium carbonate skeletons (biochemical pathways) (Savannah)

Structural adaptations in different marine organisms
Diverse algae exhibit distinct mechanisms of CaCO3 formation, with calcification occurring internally or externally. The partial reaction of calcification suggests a potential physiological role in providing H+ for CO2 production or other H+ requiring processes. Phytoplankton species relying on CO2 diffusion for photosynthesis may face limitations due to CO2 concentration and diffusion to the chloroplast's Rubisco site. Some algae have evolved mechanisms for utilizing external HCO32 as a carbon substrate, facilitated by carbonic anhydrase. The giant-celled brackish-water alga Chara deposits bands of external CaCO3 in alkaline regions, suggesting spatial separation of H+ regions involved in calcification. Calcifying macroalgae like Halimeda and Corallina also produce CaCO3 in alkaline extracellular spaces.

Coccolithophorid phytoplankton forms 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 and calcification mechanisms underscores these organisms' adaptability and complexity in responding to environmental factors.

Evolution of biogenic calcification (Savannah)
The evolution of biogenic calcification and carbonate structures within the eukaryotic domain is a complex narrative, highlighted by the distribution of mineralized skeletons across major clades, as depicted in Figure 2. In Figure 2, 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 for echinoderm and ascidian skeletons is less clear, but a conservative estimate indicates that carbonate skeletons evolved at least twenty-eight times within Euckarya. 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.

Corals
Blue Linckia Starfish

Corals are an obvious group of calcifying organisms, a group that easily comes to mind when one thinks of tropical oceans, scuba diving, and of course the Great Barrier Reef off the coast of Australia. 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. Coral reefs uptake calcium and carbonate from the water to form calcium carbonate via the following chemical reaction:

CO32- + Ca2+ → CaCO3

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 CaCO3 precipitation that exist naturally in seawater. Dissolved inorganic carbon (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 than in corals that do not have this symbiotic relationship. The coral algal symbionts, Symbiodinium sp., show decreased populations with increased temperatures, often leaving the coral colorless and unable to photosynthesize and losing pigments (known as coral bleaching) [1] Echinoderms, of the phylum Echinodermata, include sea creatures such as sea stars, sea urchins, sand dollars, crinoids, sea cucumbers and brittle stars. This group of organisms is known for their radial symmetry and they mostly use the intracellular calcifying strategy, keeping their calcified structures inside their bodies. They form large vesicles from the fusing of their cell membranes and inside these vesicles is where the calcified crystals are formed. The mineral is only exposed to the environment once those cell membranes are degraded, and therefore serve as a sort of skeleton.

The echinoderm skeleton is an endoskeleton that is enclosed by the epidermis. These structures are made of interlocking calcium carbonate plates, which can either fit tightly together, as in the case of sea urchins, or can be loosely bound, such as in the case of starfish. The epidermis or skin covering the calcium carbonate plates are able to uptake and secrete nutrients in order to support and maintain the skeleton. The epidermis usually also contains pigment cells to give the organism color, can detect motion of small creatures on the animal’s surface, and also generally contain gland cells to secrete fluids or toxins. These calcium carbonate plates and skeletons provide the organism structure, support, and protection.

Crustaceans
Chthamalus stellatus

As anyone who has eaten a crab or lobster knows, crustaceans have a hard outer shell. The crustacean will form a network of chitin-protein fibers and then will precipitate calcium carbonate within this matrix of fibers. These chitin-protein fibers are first hardened by sclerotization, or crosslinking of protein and polysaccharides and of proteins with other proteins before the calcification process begins. The calcium carbonate component makes up between 20 and 50% of the shell. The presence of a hard, calcified exoskeleton means that the crustacean has to molt and shed the exoskeleton as its body size increases. This links the calcification process to the molting cycles, making a regular source of calcium and carbonate ions crucial. The crustacean is the only phylum of animals that can resorb calcified structures, and will reabsorb minerals from the old shell and incorporate them into the new shell. 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, and between the molting cycles the crustacean must avoid predators while it waits for the calcite shell to form and harden. Phytoplankton, especially haptophytes such as coccolithophores, are also well known for their calcium carbonate production. It is estimated that these phytoplankton may contribute up to 70% to the global calcium carbonate precipitation, and coccolithophores are the largest phytoplankton contributors. Contributing between 1 and 10% of total primary productivity, 200 species of coccolithophores live in the ocean, and under the right conditions they can form large blooms in subpolar regions. 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.

Calcifying rhodophytes stock their filamentous cell walls with calcium carbonate and magnesium[2]. Corallinales is the one genus of red algae that exists but their distribution ranges across the world's oceans[3]. Examples include Corallina, Neogoniolithon, and Harveylithon[3]. The magnesium-rich calcium carbonate of Corallinales cell wall provides shelter from predators and structural integrity in the intertidal zone[4][5][6]. The CaCO3 production in Coralline also plays a role in habitat formation and provides resources for benthic invertebrates[5].

Calcifying bacteria
Evidence shows that some calcifying cyanobacteria strains have existed for millions of years and contributed to large land formations[7]. About 70 strains of cyanobacteria can precipitate calcium carbonate, including some strains of Synechococcus, Bacillus sphaericus, Bactilus subtilus,and Sporosarcina psychrophile[8][9].

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 it is produced biologically in the upper layer of the ocean (Sarmiento & Gruber). CaCO3 material is exported from the upper ocean to sediments on the ocean floor where it either dissolves or is buried (Sarmiento & Gruber). Alternatively, CaCO3 can dissolve or be remineralized within the water column prior to reaching the seafloor.''

(image)

''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. Mineral CaCO3 is more commonly found in shallow, benthic regions of the ocean where the environment is supersaturated with respect to calcite. CaCO3 is less commonly found, if at all, in sediments in the pelagic zone, or deep open ocean. The deep ocean sediments are typically undersaturated with respect to CaCO3.''

Impact of OA on Marine Calcification
''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 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.''

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, reaching approximately 740 ppmv 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.

Beyond the direct effects on calcification, it underscores the collateral consequences of OA on shell surfaces. Damaged shell surfaces, primarily resulting from reduced calcification rates, contribute to a significant decrease in sale prices, marking a critical economic concern. Researched financial assessments reveal that such damages, particularly impacting culture quasi-profits, 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 100 billion USD. 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
The degradation of coral reefs, coupled with ocean acidification, can adversely affect marine organisms relying on calcification processes, potentially disrupting entire ecosystems. As these 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 diverse 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, surpassing global dependence, with the sector contributing to over 15 percent of GDP and sustaining 13 percent of jobs in the area. Amidst these challenges, the global economic value of coral reefs becomes evident, estimated at $490 USD/year for an average hectare. Specific regions showcase the economic significance of coral reefs, with Hawai'i's contributing $360 million USD annually to its economy, and the Philippine economy receiving at least $1.06 billion USD 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.