Biological pump

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The biological pump (or marine biological carbon pump) is the ocean's biologically driven sequestration of carbon from the atmosphere and land runoff to the ocean interior and seafloor sediments. In other words, it is a biologically mediated process which results in the sequestering of carbon in the deep ocean away from the atmosphere and the land. The biological pump is the biological component of the "marine carbon pump" which contains both a physical and biological component. It is the part of the broader oceanic carbon cycle responsible for the cycling of organic matter formed mainly by phytoplankton during photosynthesis (soft-tissue pump), as well as the cycling of calcium carbonate (CaCO₃) formed into shells by certain organisms such as plankton and mollusks (carbonate pump).

Budget calculations of the biological carbon pump are based on the ratio between sedimentation (carbon export to the ocean floor) and remineralization (release of carbon to the atmosphere).

The biological pump is not so much the result of a single process, but rather the sum of a number of processes each of which can influence biological pumping. Overall, the pump transfers about 10.2 gigatonnes of carbon every year into the ocean's interior and a total of 1300 gigatonnes carbon over an average 127 years. This takes carbon out of contact with the atmosphere for several thousand years or longer. An ocean without a biological pump would result in atmospheric carbon dioxide levels about 400 ppm higher than the present day.

Overview

The element carbon plays a central role in climate and life on Earth. It is capable of moving among and between the geosphere, cryosphere, atmosphere, biosphere and hydrosphere. This flow of carbon is referred to as the Earth's carbon cycle. It is also intimately linked to the cycling of other elements and compounds. The ocean plays a fundamental role in Earth's carbon cycle, helping to regulate atmospheric CO₂ concentration. The biological pump is a set of processes that transfer organic carbon from the surface to the deep ocean, and is at the heart of the ocean carbon cycle.

The biological pump can be divided into three distinct phases, the first of which is the production of fixed carbon by planktonic phototrophs in the euphotic (sunlit) surface region of the ocean. In these surface waters, phytoplankton use carbon dioxide (CO₂), nitrogen (N), phosphorus (P), and other trace elements (barium, iron, zinc, etc.) during photosynthesis to make carbohydrates, lipids, and proteins. Some plankton, (e.g. coccolithophores and foraminifera) combine calcium (Ca) and dissolved carbonates (carbonic acid and bicarbonate) to form a calcium carbonate (CaCO₃) protective coating.

thumb|upright=1.203| Photic zone: 0–100 m; Mesopelagic: 100–1000 m; Bathypelagic: 1000 to abyssal depths. Below 1000 m depth carbon is considered removed from the atmosphere for at least 100 years. Scavenging: DOC incorporation within sinking particles. thumb|upright=2.2|left|

Once this carbon is fixed into soft or hard tissue, the organisms either stay in the euphotic zone to be recycled as part of the regenerative nutrient cycle or once they die, continue to the second phase of the biological pump and begin to sink to the ocean floor. The sinking particles will often form aggregates as they sink, which greatly increases the sinking rate. It is this aggregation that gives particles a better chance of escaping predation and decomposition in the water column and eventually making it to the sea floor.<br /><small>Adapted from Simon et al., 2002.</small>]]

The first step in the biological pump is the synthesis of both organic and inorganic carbon compounds by phytoplankton in the uppermost, sunlit layers of the ocean. Organic compounds in the form of sugars, carbohydrates, lipids, and proteins are synthesized during the process of photosynthesis:

CO₂ + H₂O + light → CH₂O + O₂

In addition to carbon, organic matter found in phytoplankton is composed of nitrogen, phosphorus and various trace metals. The ratio of carbon to nitrogen and phosphorus varies from place to place, but has an average ratio near 106C:16N:1P, known as the Redfield ratio. Trace metals such as magnesium, cadmium, iron, calcium, barium and copper are orders of magnitude less prevalent in phytoplankton organic material, but necessary for certain metabolic processes and therefore can be limiting nutrients in photosynthesis due to their lower abundance in the water column.]]

Dissolved and particulate carbon

Phytoplankton supports all life in the ocean as it converts inorganic compounds into organic constituents. This autotrophically produced biomass presents the foundation of the marine food web.

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thumb|upright=2|right| Black arrows represent DIC produced by PIC dissolution. Grey lines represent terrestrial PIC. <small>Units are Tg C y⁻¹</small>

Ocean carbon pools

The marine biological pump depends on a number of key pools, components and processes that influence its functioning. There are four main pools of carbon in the ocean.

• Dissolved inorganic carbon (DIC) is the largest pool. It constitutes around 38,000 Pg C and includes dissolved carbon dioxide (CO₂), bicarbonate (), carbonate (), and carbonic acid (). The equilibrium between carbonic acid and carbonate determines the pH of the seawater. Carbon dioxide dissolves easily in water and its solubility is inversely related to temperature. Dissolved CO₂ is taken up in the process of photosynthesis, and can reduce the partial pressure of CO₂ in the seawater, favouring drawdown from the atmosphere. The reverse process respiration, releases CO₂ back into the water, can increase partial pressure of CO₂ in the seawater, favouring release back to the atmosphere. The formation of calcium carbonate by organisms such as coccolithophores has the effect of releasing CO₂ into the water. DOC can be classified according to its reactivity as refractory, semi-labile or labile. The labile pool constitutes around 0.2 Pg C, is bioavailable, and has a high production rate (~ 15−25 Pg C y⁻¹). The refractory component is the biggest pool (~642 Pg C ± 32; and is relatively small compared with DIC and DOC. Though small in size, this pool is highly dynamic, having the highest turnover rate of any organic carbon pool on the planet. Driven by primary production, it produces around 50 Pg C y⁻¹ globally. It can be separated into living (e.g. phytoplankton, zooplankton, bacteria) and non-living (e.g. detritus) material. Of these, the phytoplankton carbon is particularly important, because of its role in marine primary production, and also because it serves as the food resource for all the larger organisms in the pelagic ecosystem. It is present in the form of calcium carbonate (CaCO₃) in particulate form, and impacts the carbonate system and pH of the seawater. Estimates for PIC production are in the region of 0.8–1.4 Pg C y⁻¹, with at least 65% of it being dissolved in the upper water column, the rest contributing to deep sediments. Coccolithophores and foraminifera are estimated to be the dominant sources of PIC in the open ocean. This biologically fixed carbon is used as a protective coating for many planktonic species (coccolithophores, foraminifera) as well as larger marine organisms (mollusk shells). Calcium carbonate is also excreted at high rates during osmoregulation by fish, and can form in whiting events. While this form of carbon is not directly taken from the atmospheric budget, it is formed from dissolved forms of carbonate which are in equilibrium with CO₂ and then responsible for removing this carbon via sequestration.

CO₂ + H₂O → H₂CO₃ → H⁺ + HCO₃⁻

Ca²⁺ + 2HCO₃⁻ → CaCO₃ + CO₂ + H₂O

While this process does manage to fix a large amount of carbon, two units of alkalinity are sequestered for every unit of sequestered carbon. The formation and sinking of CaCO₃ therefore drives a surface to deep alkalinity gradient which serves to raise the pH of surface waters, shifting the speciation of dissolved carbon to raise the partial pressure of dissolved CO₂ in surface waters, which actually raises atmospheric levels. In addition, the burial of CaCO₃ in sediments serves to lower overall oceanic alkalinity, tending to raise pH and thereby atmospheric CO₂ levels if not counterbalanced by the new input of alkalinity from weathering.

Oceanic carbon cycle

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Three main processes (or pumps) that make up the marine carbon cycle bring atmospheric carbon dioxide (CO₂) into the ocean interior and distribute it through the oceans. These three pumps are: (1) the solubility pump, (2) the carbonate pump, and (3) the biological pump. The total active pool of carbon at the Earth's surface for durations of less than 10,000 years is roughly 40,000 gigatons C (Gt C, a gigaton is one billion tons, or the weight of approximately 6 million blue whales), and about 95% (~38,000 Gt C) is stored in the ocean, mostly as dissolved inorganic carbon. The speciation of dissolved inorganic carbon in the marine carbon cycle is a primary controller of acid-base chemistry in the oceans.

Solubility pump

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The biological pump is accompanied by a physico-chemical counterpart known as the solubility pump. This pump transports significant amounts of carbon in the form of dissolved inorganic carbon (DIC) from the ocean's surface to its interior. It involves physical and chemical processes only, and does not involve biological processes.

The solubility pump is driven by the coincidence of two processes in the ocean:

• The solubility of carbon dioxide is a strong inverse function of seawater temperature (i.e. solubility is greater in cooler water)
• The thermohaline circulation is driven by the formation of deep water at high latitudes where seawater is usually cooler and denser

Since deep water (that is, seawater in the ocean's interior) is formed under the same surface conditions that promote carbon dioxide solubility, it contains a higher concentration of dissolved inorganic carbon than might be expected from average surface concentrations. Consequently, these two processes act together to pump carbon from the atmosphere into the ocean's interior. One consequence of this is that when deep water upwells in warmer, equatorial latitudes, it strongly outgasses carbon dioxide to the atmosphere because of the reduced solubility of the gas.

Carbonate pump

The carbonate pump is sometimes referred to as the "hard tissue" component of the biological pump. Some surface marine organisms, like coccolithophores, produce hard structures out of calcium carbonate, a form of particulate inorganic carbon, by fixing bicarbonate. This fixation of DIC is an important part of the oceanic carbon cycle.

Ca²⁺ + 2 HCO₃⁻ → CaCO₃ + CO₂ + H₂O

While the biological carbon pump fixes inorganic carbon (CO₂) into particulate organic carbon in the form of sugar (C₆H₁₂O₆), the carbonate pump fixes inorganic bicarbonate and causes a net release of CO₂.

Continental shelf pump

The continental shelf pump is proposed as operating in the shallow waters of the continental shelves as a mechanism transporting carbon (dissolved or particulate) from the continental waters to the interior of the adjacent deep ocean. As originally formulated, the pump is thought to occur where the solubility pump interacts with cooler, and therefore denser water from the shelf floor which feeds down the continental slope into the neighbouring deep ocean. The dense, carbon-rich shelf waters then sink to the shelf floor and enter the sub-surface layer of the open ocean via isopycnal mixing.

Processes in the biological pump

thumb|upright=2.2|right| Budget calculations of the biological carbon pump are based on the ratio between [[Marine sediment|sedimentation (carbon export) and remineralization (release to the atmosphere). A single phytoplankton cell has a sinking rate around one metre per day. Given that the average depth of the ocean is about four kilometres, it can take over ten years for these cells to reach the ocean floor. However, through processes such as coagulation and expulsion in predator fecal pellets, these cells form aggregates. These aggregates, known as marine snow, have sinking rates orders of magnitude greater than individual cells and complete their journey to the deep in a matter of days.

Of the 50–60 Pg of carbon fixed annually, roughly 10% leaves the surface mixed layer of the oceans, while less than 0.5% of eventually reaches the sea floor.

Budget calculations of the biological carbon pump are based on the ratio between sedimentation (carbon export) and remineralization (release to the atmosphere). It has been estimated that sinking particles export up to 25% of the carbon captured by phytoplankton in the surface ocean to deeper water layers. About 20% of this export (5% of surface values) is buried in the ocean sediments mainly due to their mineral ballast. Formation and sinking of these aggregates drive the biological carbon pump via export and sedimentation of organic matter from the surface mixed layer to the deep ocean and sediments. The fraction of organic matter that leaves the upper mixed layer of the ocean is, among other factors, determined by the sinking velocity and microbial remineralisation rate of these aggregates. Recent observations have shown that the fluxes of ballast minerals (calcium carbonate, opal, and lithogenic material) and the organic carbon fluxes are closely correlated in the bathypelagic zones of the ocean. This has led to the hypothesis that organic carbon export is determined by the presence of ballast minerals within settling aggregates.

Mineral ballasting is associated with about 60% of the flux of particulate organic carbon (POC) in the high-latitude North Atlantic, and with about 40% of the flux in the Southern Ocean. Strong correlations exist also in the deep ocean between the presence of ballast minerals and the flux of POC. This suggests ballast minerals enhance POC flux by increasing the sink rate of ballasted aggregates. Ballast minerals could additionally provide aggregated organic matter some protection from degradation.

It has been proposed that organic carbon is better preserved in sinking particles due to increased aggregate density and sinking velocity when ballast minerals are present and/or via protection of the organic matter due to quantitative association to ballast minerals. Carbon-specific respiration rates in pellets, however, were similar and independent of mineral content. These results suggest differences in mineral composition do not lead to differential protection of POC against microbial degradation, but the enhanced sinking velocities may result in up to 10-fold higher carbon preservation in pellets containing biogenic minerals as compared to that of pellets without biogenic minerals and may even act as a catalyst in aggregate formation. However, it has also been shown that incorporation of minerals can cause aggregates to fragment into smaller and denser aggregates. This can potentially lower the sinking velocity of the aggregated organic material due to the reduced aggregate sizes, and, thus, lower the total export of organic matter. Conversely, if the incorporation of minerals increases the aggregate density, its size-specific sinking velocity may also increase, which could potentially increase the carbon export. Therefore, there is still a need for better quantitative investigations of how the interactions between minerals and organic aggregates affect the degradation and sinking velocity of the aggregates and, hence, carbon sequestration in the ocean. while that value is <0.5% in the open oceans on average. Therefore, most of nutrients remain in the water column, recycled by the biota. Heterotrophic organisms will utilize the materials produced by the autotrophic (and chemotrophic) organisms and via respiration will remineralise the compounds from the organic form back to inorganic, making them available for primary producers again.

For most areas of the ocean, the highest rates of carbon remineralisation occur at depths between in the water column, decreasing down to about where remineralisation rates remain pretty constant at 0.1 μmol kg⁻¹ yr⁻¹. This provides the most nutrients available for primary producers within the photic zone, though it leaves the upper surface waters starved of inorganic nutrients. Most remineralisation is done with dissolved organic carbon (DOC). Studies have shown that it is larger sinking particles that transport matter down to the sea floor while suspended particles and dissolved organics are mostly consumed by remineralisation. This happens in part due to the fact that organisms must typically ingest nutrients smaller than they are, often by orders of magnitude. With the microbial community making up 90% of marine biomass, it is particles smaller than the microbes (on the order of ) that will be taken up for remineralisation.

Key role of phytoplankton

Marine phytoplankton perform half of all photosynthesis on Earth and directly influence global biogeochemical cycles and the climate, yet how they will respond to future global change is unknown. Carbon dioxide is one of the principal drivers of global change and has been identified as one of the major challenges in the 21st century. Carbon dioxide (CO₂) generated during anthropogenic activities such as deforestation and burning of fossil fuels for energy generation rapidly dissolves in the surface ocean and lowers seawater pH, while CO₂ remaining in the atmosphere increases global temperatures and leads to increased ocean thermal stratification. While CO₂ concentration in the atmosphere is estimated to be about 270 ppm before the industrial revolution, it has currently increased to about 400 ppm and is expected to reach 800–1000 ppm by the end of this century according to the "business as usual" CO₂ emission scenario. While the solubility pump serves to concentrate dissolved inorganic carbon (CO₂ plus bicarbonate and carbonate ions) in the deep oceans, the biological carbon pump (a key natural process and a major component of the global carbon cycle that regulates atmospheric CO₂ levels) transfers both organic and inorganic carbon fixed by primary producers (phytoplankton) in the euphotic zone to the ocean interior and subsequently to the underlying sediments. Thus, the biological pump takes carbon out of contact with the atmosphere for several thousand years or longer and maintains atmospheric CO₂ at significantly lower levels than would be the case if it did not exist. An ocean without a biological pump, which transfers roughly 11 Gt C yr⁻¹ into the ocean's interior, would result in atmospheric CO₂ levels ~400 ppm higher than present day. which attenuates exponentially towards the base of the mesopelagic zone and only about 1% of the surface production reaches the sea floor. This deep-ocean DIC returns to the atmosphere on millennial timescales through thermohaline circulation. Ballast minerals (silicate and carbonate biominerals and dust) are the major constituents of particles that leave the ocean surface via sinking. They are typically denser than seawater and most organic matter, thus, providing a large part of the density differential needed for sinking of the particles. Discarded appendicularian houses are highly abundant (thousands per m3 in surface waters) and are microbial hotspots with high concentrations of bacteria, ciliates, flagellates and phytoplankton. These discarded houses are therefore among the most important sources of aggregates directly produced by zooplankton in terms of carbon cycling potential. The main functional groups of marine phytoplankton that contribute to export production include nitrogen fixers (diazotrophic cyanobacteria), silicifiers (diatoms) and calcifiers (coccolithophores). Each of these phytoplankton groups differ in the size and composition of their cell walls and coverings, which influence their sinking velocities. For example, autotrophic picoplankton (0.2–2&nbsp;μm in diameter)—which include taxa such as cyanobacteria (e.g., Prochlorococcus spp. and Synechococcus spp.) and prasinophytes (various genera of eukaryotes <2&nbsp;μm)—are believed to contribute much less to carbon export from surface layers due to their small size, slow sinking velocities (<0.5 m/day) and rapid turnover in the microbial loop. In contrast, larger phytoplankton cells such as diatoms (2–500&nbsp;μm in diameter) are very efficient in transporting carbon to depth by forming rapidly sinking aggregates. According to the reports of Miklasz and Denny, the sinking velocities of diatoms can range from 0.4 to 35 m/day. Saba et al. (2009) and Steinberg et al. (2017).</small>

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| image2 = Copepod faecal pellet production in the deep ocean.png

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| caption2 = On the left above, intact fecal pellets reach the deep ocean via vertical migration of zooplankton, whereas on the right fecal pellets at depth result from in situ repackaging of sinking detritus by deep-dwelling zooplankton. Actual mechanisms are likely to include both scenarios.

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