Biogenic silica

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Diatoms are capable of synthesizing silica glass in vivo. Diatoms through the microscope.jpg
Diatoms are capable of synthesizing silica glass in vivo.

Biogenic silica (bSi), also referred to as opal, biogenic opal, or amorphous opaline silica, forms one of the most widespread biogenic minerals. For example, microscopic particles of silica called phytoliths can be found in grasses and other plants. Silica is an amorphous metal oxide formed by complex inorganic polymerization processes. This is opposed to the other major biogenic minerals, comprising carbonate and phosphate, which occur in nature as crystalline iono-covalent solids (e.g. salts) whose precipitation is dictated by solubility equilibria. [1] Chemically, bSi is hydrated silica (SiO2·nH2O), which is essential to many plants and animals.


Silica in marine environments

Silicate, or silicic acid (H4SiO4), is an important nutrient in the ocean. Unlike the other major nutrients such as phosphate, nitrate, or ammonium, which are needed by almost all marine plankton, silicate is an essential chemical requirement for very specific biota, including diatoms, radiolaria, silicoflagellates, and siliceous sponges. These organisms extract dissolved silicate from open ocean surface waters for the buildup of their particulate silica (SiO2), or opaline, skeletal structures (i.e. the biota's hard parts). [2] [3] Some of the most common siliceous structures observed at the cell surface of silica-secreting organisms include: spicules, scales, solid plates, granules, frustules, and other elaborate geometric forms, depending on the species considered. [4]

Five major sources of dissolved silica to the marine environment can be distinguished: [3]

Once the organism has perished, part of the siliceous skeletal material dissolves, as it settles through the water column, enriching the deep waters with dissolved silica. [3] Some of the siliceous scales can also be preserved over time as microfossils in deep-sea sediments, providing a window into modern and ancient plankton/protists communities. [4] This biologic process has operated, since at least early Paleozoic time, to regulate the balance of silica in the ocean: Radiolarians (Cambrian/Ordovician-Holocene), diatoms (Cretaceous-Holocene), and silicoflagellates (Cretaceous-Holocene) form the ocean's main contributors to the global silica biogenic cycle throughout geologic time. Diatoms account for 43% of the ocean primary production, and are responsible for the bulk of silica extraction from ocean waters in the modern ocean, and during much of the past fifty million years. In contrast, oceans of Jurassic and older ages, were characterized by radiolarians as major silica-utilizing phyla. [2] Nowadays, radiolarians are the second (after diatoms) major producers of suspended amorphous silica in ocean waters. Their distribution ranges from the Arctic to the Antarctic, being most abundant in the equatorial zone. In equatorial Pacific waters, for example, about 16,000 specimens per cubic meter can be observed. [4]

Silicate cycling gained increasingly in scientific attention the past decade because of following reasons. Firstly, the modern marine silica cycle is widely believed to be dominated by diatoms for the fixation and export of particulate matter (including organic carbon), from the euphotic zone to the deep ocean, via a process known as the biological pump. As a result, diatoms, and other silica-secreting organisms, play a crucial role in the global carbon cycle, and have the ability to affect atmospheric CO2 concentrations on a variety of time scales, by sequestering CO2 in the ocean. This connection between biogenic silica and organic carbon, together with the significantly higher preservation potential of biogenic siliceous compounds, compared to organic carbon, makes opal accumulation records very interesting for paleoceanography and paleoclimatology. Secondly, biogenic silica accumulation on the sea floor contains lot of information about where in the ocean export production has occurred on time scales ranging from hundreds to millions of years. For this reason, opal deposition records provide valuable information regarding large-scale oceanographic reorganizations in the geological past, as well as paleoproductivity. And last, the mean oceanic residence time for silicate is approximately 10,000–15,000 yr. This relative short residence time, makes oceanic silicate concentrations and fluxes sensitive to glacial/interglacial perturbations, and thus an excellent proxy for evaluating climate changes. [3] [5]

The remains of diatoms and other silica-utilizing organisms are found, as opal sediments within pelagic deep-sea deposits. Pelagic sediments, containing significant quantities of siliceous biogenic remains, are commonly referred to as siliceous ooze. Siliceous ooze are particularly abundant in the modern ocean at high latitudes in the northern and southern hemispheres. A striking feature of siliceous ooze distribution is a ca. 200 km wide belt stretching across the Southern Ocean. Some equatorial regions of upwelling, where nutrients are abundant and productivity is high, are also characterized by local siliceous ooze. Siliceous oozes are composed primarily of the remains of diatoms and radiolarians, but may also include other siliceous organisms, such as silicoflagellates and sponge spicules. Diatom ooze occurs mainly in high-latitude areas and along some continental margins, whereas radiolarian ooze are more characteristic of equatorial areas. Siliceous ooze are modified and transformed during burial into bedded cherts. [2]

Diatoms in both fresh and salt water extract silica from the water to use as a component of their cell walls. Likewise, some holoplanktonic protozoa (Radiolaria), some sponges, and some plants (leaf phytoliths) use silicon as a structural material. Silicon is known to be required by chicks and rats for growth and skeletal development. Silicon is in human connective tissues, bones, teeth, skin, eyes, glands and organs.

BSi is silica that originates from the production out of dissolved silica. BSi can either be accumulated "directly" in marine sediments (via export) or be transferred back into dissolved silica in the water column.

Increasingly, isotope ratios of oxygen (O18:O16) and silicon (Si30:Si28) are analysed from BSi preserved in lake and marine sediments to derive records of past climate change and nutrient cycling (De La Rocha, 2006; Leng and Barker, 2006). This is a particularly valuable approach considering the role of diatoms in global carbon cycling. In addition, isotope analyses from BSi are useful for tracing past climate changes in regions such as in the Southern Ocean, where few biogenic carbonates are preserved.

Marine biogenic silica budget

Rivers and submarine hydrothermal emanations supply 6.1 × 1014 g SiO2 yr−1 to the marine environment. Approximately two-thirds of this silica input is stored in continental margin and deep-sea deposits. Siliceous deep-sea sediments located beneath the Antarctic Convergence (convergence zone) host some 25% of the silica supplied to the oceans (i.e. 1.6 × 1014 g SiO2 yr−1) and consequently form one of Earth's major silica sinks. The highest biogenic silica accumulation rates in this area are observed in the South Atlantic, with values as large as 53 cm.kyr−1 during the last 18,000 yr. Further, extensive biogenic silica accumulation has been recorded in the deep-sea sediments of the Bering Sea, Sea of Okhotsk, and Subarctic North Pacific. Total biogenic silica accumulation rates in these regions amounts nearly 0.6 × 1014 g SiO2 yr−1, which is equivalent to 10% of the dissolved silica input to the oceans. Continental margin upwelling areas, such as the Gulf of California, the Peru and Chile coast, are characteristic for some of the highest biogenic silica accumulation rates in the world. For example, biogenic silica accumulation rates of 69 g SiO2/cm2/kyr have been reported for the Gulf of California. Due to the laterally confined character of these rapid biogenic silica accumulation zones, upwelling areas solely account for approximately 5% of the dissolved silica supplied to the oceans. At last, extremely low biogenic silica accumulation rates have been observed in the extensive deep-sea deposits of the Atlantic, Indian and Pacific Oceans, rendering these oceans insignificant for the global marine silica budget. [6]

Major silica sinks in the modern oceans

Large-scale oceanic circulation has a direct impact on opal deposition. The Pacific (characterized by nutrient poor surface waters, and deep nutrient rich waters) and Atlantic Ocean circulations, are favoring the production/preservation of silica and carbonate, respectively. For instance, Si/N and Si/P ratios increase from the Atlantic to the Pacific and Southern Ocean, favoring opal versus carbonate producers. Consequently, the modern configuration of large-scale oceanic circulation resulted in the localization of major opal burial zones in the Equatorial Pacific, in the eastern boundary current upwelling systems, and by far the most important, the Southern Ocean. [5]

Waters from the modern Pacific and Southern ocean, typically observe an increase in Si/N ratio at intermediate depth, which results in an increase in opal export (~ increase in opal production). In the Southern Ocean and North Pacific, this relationship between opal export and Si/N ratio switches from linear to exponential for Si/N ratios greater than 2. This gradual increase in the importance of silicate (Si) relative to nitrogen (N) has tremendous consequences for the ocean biological production. The change in nutrient ratios contributes to select diatoms as main producers, compared to other (e.g., calcifying) organisms. For example, microcosm experiments have demonstrated that diatoms are DSi supercompetitors and dominate other producers above 2 μM DSi. Consequently, opal vs. carbonate export will be favored, resulting in increasing opal production. The Southern Ocean and the North Pacific also display maximum biogenic silicate/Corganic flux ratios, and consist thus in an enrichment in biogenic silicate, compared to Corganic export flux. This combined increase in opal preservation and export makes the Southern Ocean the most important sink for DSi today. [5]

In the modern Pacific and Southern Ocean, intermediate and deep waters are characterized by a higher content in DSi, compared to the Atlantic Ocean. This interbasin difference in DSi has the effect of increasing the preservation potential of opal in the Pacific and Southern Ocean compared to their Atlantic counterparts. Atlantic DSi depleted waters tends to produce relatively less silicified organisms, which has a strong influence on the preservation of their frustules. This mechanism in best illustrated when comparing the Peru and northwest Africa upwelling systems. The dissolution/production ratio is much higher in the Atlantic upwelling than in the Pacific upwelling. This is due to the fact that coastal upwelling source waters are much richer in DSi off Peru, than off NW Africa. [5]

Cycling and accumulation of biogenic silica in the Southern Ocean sediments

Southern Ocean sediments are a major sink for biogenic silica (50-75% of the oceanic total of 4.5 × 1014 g SiO2 yr−1; DeMaster, 1981), but only a minor sink for organic carbon (<1% of the oceanic 2 × 1014 g of organic C yr−1). These relatively high rates of biogenic silica accumulation in the Southern Ocean sediments (predominantly beneath the Polar Front) relative to organic carbon (60:1 on a weight basis) results from the preferential preservation of biogenic silica in the Antarctic water column. In contrast to what was previously thought, these high rates of biogenic silica accumulation are not the result from high rates of primary production. Biological production in the Southern Ocean is strongly limited due to the low levels of irradiance coupled with deep mixed layers and/or by limited amounts of micronutrients, such as iron. [7] This preferential preservation of biogenic silica relative to organic carbon is evident in the steadily increasing ratio of silica/organic C as function of depth in the water column. About thirty-five percent of the biogenic silica produced in the euphotic zone survives dissolution within the surface layer; whereas only 4% of the organic carbon escapes microbial degradation in these near-surface waters. Consequently, considerable decoupling of organic C and silica occurs during settling through the water column. The accumulation of biogenic silica in the seabed represents 12% of the surface production, whereas the seabed organic-carbon accumulation rate accounts for solely <0.5% of the surface production. As a result, polar sediments account for most of the ocean's biogenic silica accumulation, but only a small amount of the sedimentary organic-carbon flux. [7]

BSi production

Diatomaceous earth as viewed under bright field illumination on a light microscope. Diatomaceous earth is made up of diatom cell walls, an example of biogenic silica. Silica is synthesised in the diatom cell by the polymerisation of silicic acid. This image of diatomaceous earth particles in water is at a scale of 6.236 pixels/mm, the entire image covers a region of approximately 1.13 by 0.69 mm. Diatomaceous Earth BrightField.jpg
Diatomaceous earth as viewed under bright field illumination on a light microscope. Diatomaceous earth is made up of diatom cell walls, an example of biogenic silica. Silica is synthesised in the diatom cell by the polymerisation of silicic acid. This image of diatomaceous earth particles in water is at a scale of 6.236 pixels/μm, the entire image covers a region of approximately 1.13 by 0.69 mm.

The mean daily BSi rate strongly depends on the region:

Likewise, the integrated annual BSi production strongly depends on the region:

BSi production is controlled by:

BSi dissolution

BSi dissolution is controlled by:

BSi preservation

BSi preservation is measured by:

BSi preservation is controlled by:

Opaline silica on Mars

In the Gusev crater of Mars, the Mars Exploration Rover Spirit inadvertently discovered opaline silica. One of its wheels had earlier become immobilized and thus was effectively trenching the Martian regolith as it dragged behind the traversing rover. Later analysis showed that the silica was evidence for hydrothermal conditions. [8]

Related Research Articles

Diatom A class of microalgae, found in the oceans, waterways and soils of the world

Diatoms are a major group of algae, specifically microalgae, found in the oceans, waterways and soils of the world. Living diatoms makeup a significant portion of the Earth's biomass: they generate about 20 - 50 percent of the oxygen produced on the planet each year, take in over 6.7 billion metric tons of silicon each year from the waters in which they live, and contribute nearly half of the organic material found in the oceans. The shells of dead diatoms can reach as much as a half-mile (800m) deep on the ocean floor, and the entire Amazon basin is fertilized annually by 27 million tons of diatom shell dust transported by transatlantic winds from the African Sahara, much of it from the Bodélé Depression, which was once made up a system of fresh-water lakes.

Chert A hard, fine-grained sedimentary rock composed of crystals of quartz (silica) that are very small

Chert is a hard, fine-grained sedimentary rock composed of crystals of quartz (silica) that are very small (microcrystalline or cryptocrystalline). Quartz (silica) is the mineral form of silicon dioxide (SiO2). Chert is often of biological origin (organic) but may also occur inorganically as a chemical precipitate or a diagenetic replacement (e.g., petrified wood). Geologists use chert as a generic name for any type of microcrystalline or cryptocrystalline quartz.

High-nutrient, low-chlorophyll (HNLC) regions are regions of the ocean where the abundance of phytoplankton is low and fairly constant despite the availability of macronutrients. Phytoplankton rely on a suite of nutrients for cellular function. Macronutrients are generally available in higher quantities in surface ocean waters, and are the typical components of common garden fertilizers. Micronutrients are generally available in lower quantities and include trace metals. Macronutrients are typically available in millimolar concentrations, while micronutrients are generally available in micro- to nanomolar concentrations. In general, nitrogen tends to be a limiting ocean nutrient, but in HNLC regions it is never significantly depleted. Instead, these regions tend to be limited by low concentrations of metabolizable iron. Iron is a critical phytoplankton micronutrient necessary for enzyme catalysis and electron transport.

Calcareous An adjective meaning mostly or partly composed of calcium carbonate

Calcareous is an adjective meaning "mostly or partly composed of calcium carbonate", in other words, containing lime or being chalky. The term is used in a wide variety of scientific disciplines.

Carbonate compensation depth (CCD) is the depth in the oceans below which the rate of supply of calcite lags behind the rate of solvation, such that no calcite is preserved. Aragonite compensation depth describes the same behaviour in reference to aragonitic carbonates. Aragonite is more soluble than calcite, so the aragonite compensation depth is generally shallower than the calcite compensation depth.

Pelagic sediment or pelagite is a fine-grained sediment that accumulates as the result of the settling of particles to the floor of the open ocean, far from land. These particles consist primarily of either the microscopic, calcareous or siliceous shells of phytoplankton or zooplankton; clay-size siliciclastic sediment; or some mixture of these. Trace amounts of meteoric dust and variable amounts of volcanic ash also occur within pelagic sediments. Based upon the composition of the ooze, there are three main types of pelagic sediments: siliceous oozes, calcareous oozes, and red clays.

Lithogenic silica (LSi) is silica that originates from terrestrial sources of rock and soil, i.e. from silicate minerals and crystals.

f-ratio In oceanic biogeochemistry, the fraction of total primary production fuelled by nitrate

In oceanic biogeochemistry, the f-ratio is the fraction of total primary production fuelled by nitrate. The ratio was originally defined by Richard Eppley and Bruce Peterson in one of the first papers estimating global oceanic production. This fraction was originally believed significant because it appeared to directly relate to the sinking (export) flux of organic marine snow from the surface ocean by the biological pump. However, this interpretation relied on the assumption of a strong depth-partitioning of a parallel process, nitrification, that more recent measurements has questioned.

Yaquina Bay small bay partially within Newport, Oregon, United States

Yaquina Bay is a coastal estuarine community found in Newport, Oregon, United States. Yaquina Bay is a semi-enclosed body of water, approximately 8 km² (3.2 mi²) in area, with free connection to the Pacific Ocean, but also diluted with freshwater from the Yaquina River land drainage. The Bay is traversed by the Yaquina Bay Bridge. There are three small communities that border the Yaquina River and Bay; Newport, Toledo and Elk City. The Yaquina Bay in Newport is a popular tourist destination along the Pacific Coast Highway. It is also an important estuary for the ecology and economy of the area.


Radiolarite is a siliceous, comparatively hard, fine-grained, chert-like, and homogeneous sedimentary rock that is composed predominantly of the microscopic remains of radiolarians. This term is also used for indurated radiolarian oozes and sometimes as a synonym of radiolarian earth. However, radiolarian earth is typically regarded by Earth scientists to be the unconsolidated equivalent of a radiolarite. A radiolarian chert is well-bedded, microcrystalline radiolarite that has a well-developed siliceous cement or groundmass.

Microbial loop Mikrobial loop

The microbial loop describes a trophic pathway in the marine microbial food web where dissolved organic carbon (DOC) is returned to higher trophic levels via its incorporation into bacterial biomass, and then coupled with the classic food chain formed by phytoplankton-zooplankton-nekton. The term microbial loop was coined by Farooq Azam and Tom Fenchel et al. to include the role played by bacteria in the carbon and nutrient cycles of the marine environment.

Alkali–silica reaction Expansive chemical reaction damaging concrete

The alkali–silica reaction (ASR), more commonly known as "concrete cancer", is a swelling reaction that occurs over time in concrete between the highly alkaline cement paste and the reactive non-crystalline (amorphous) silica found in many common aggregates, given sufficient moisture.

Siliceous ooze

Siliceous ooze is a type of biogenic pelagic sediment located on the deep ocean floor. Siliceous oozes are the least common of the deep sea sediments, and make up approximately 15% of the ocean floor. Oozes are defined as sediments which contain at least 30% skeletal remains of pelagic microorganisms. Siliceous oozes are largely composed of the silica based skeletons of microscopic marine organisms such as diatoms and radiolarians. Other components of siliceous oozes near continental margins may include terrestrially derived silica particles and sponge spicules. Siliceous oozes are composed of skeletons made from opal silica Si(O2), as opposed to calcareous oozes, which are made from skeletons of calcium carbonate organisms (i.e. coccolithophores). Silica (Si) is a bioessential element and is efficiently recycled in the marine environment through the silica cycle. Distance from land masses, water depth and ocean fertility are all factors that affect the opal silica content in seawater and the presence of siliceous oozes.

Sponge reef

Sponge reefs are reefs formed by Hexactinellid sponges, which have a skeleton made of silica, and are often referred to as glass sponges. Such reefs are now very rare, and found only on the western Canadian continental shelf. Although common in the late Jurassic period, sponge reefs were believed to have gone extinct during or shortly after the Cretaceous period, until the existing reefs were discovered in 1987–1988 - hence these sometimes being dubbed living fossils.

The Southern Pacific Gyre is part of the Earth’s system of rotating ocean currents, bounded by the Equator to the north, Australia to the west, the Antarctic Circumpolar Current to the south, and South America to the east. The center of the South Pacific Gyre is the oceanic pole of inaccessibility, the site on Earth farthest from any continents and productive ocean regions and is regarded as Earth’s largest oceanic desert. The gyre, as with Earth's other four gyres, contains an area with elevated concentrations of pelagic plastics, chemical sludge, and other debris known as the South Pacific garbage patch.

Pelagic red clay, also known as simply red clay, brown clay or pelagic clay, is a type of pelagic sediment.

Fragilariopsis kerguelensis species of alga

Fragilariopsis kerguelensis, is a pennate diatom native to the Southern Ocean. It has been characterized as "the most abundant diatom in the Antarctic Seas".

Reverse weathering generally refers to the formation of a clay neoformation that utilizes cations and alkalinity in a process unrelated to the weathering of silicates. More specifically reverse weathering refers to the formation of authigenic clay minerals from the reaction of 1) biogenic silica with aqueous cations or cation bearing oxides or 2) cation poor precursor clays with dissolved cations or cation bearing oxides.

Nutrient cycling in the Columbia River Basin involves the transport of nutrients through the system, as well as transformations from among dissolved, solid, and gaseous phases, depending on the element. The elements that constitute important nutrient cycles include macronutrients such as nitrogen, silicate, phosphorus, and micronutrients, which are found in trace amounts, such as iron. Their cycling within a system is controlled by many biological, chemical, and physical processes.

The silica cycle is the biogeochemical cycle in which silica is transported between the Earth's systems. Opal silica (SiO2) is a chemical compound of silicon, and is also called silicon dioxide. Silicon is considered a bioessential element and is one of the most abundant elements on Earth. The silica cycle has significant overlap with the carbon cycle (see Carbonate-Silicate cycle) and plays an important role in the sequestration of carbon through continental weathering, biogenic export and burial as oozes on geologic timescales.


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