Remineralisation

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In biogeochemistry, remineralisation (or remineralization) refers to the breakdown or transformation of organic matter (those molecules derived from a biological source) into its simplest inorganic forms. These transformations form a crucial link within ecosystems as they are responsible for liberating the energy stored in organic molecules and recycling matter within the system to be reused as nutrients by other organisms. [1]

Contents

Remineralisation is normally viewed as it relates to the cycling of the major biologically important elements such as carbon, nitrogen and phosphorus. While crucial to all ecosystems, the process receives special consideration in aquatic settings, where it forms a significant link in the biogeochemical dynamics and cycling of aquatic ecosystems.

Role in biogeochemistry

The term "remineralization" is used in several contexts across different disciplines. The term is most commonly used in the medicinal and physiological fields, where it describes the development or redevelopment of mineralized structures in organisms such as teeth or bone. In the field of biogeochemistry, however, remineralization is used to describe a link in the chain of elemental cycling within a specific ecosystem. In particular, remineralization represents the point where organic material constructed by living organisms is broken down into basal inorganic components that are not obviously identifiable as having come from an organic source. This differs from the process of decomposition which is a more general descriptor of larger structures degrading to smaller structures.

Biogeochemists study this process across all ecosystems for a variety of reasons. This is done primarily to investigate the flow of material and energy in a given system, which is key to understanding the productivity of that ecosystem along with how it recycles material versus how much is entering the system. Understanding the rates and dynamics of organic matter remineralization in a given system can help in determining how or why some ecosystems might be more productive than others.

Remineralization reactions

While it is important to note that the process of remineralization is a series of complex biochemical pathways [within microbes], it can often be simplified as a series of one-step processes for ecosystem-level models and calculations. A generic form of these reactions is shown by:

The above generic equation starts with two reactants: some piece of organic matter (composed of organic carbon) and an oxidant. Most organic carbon exists in a reduced form which is then oxidized by the oxidant (such as O2) into CO2 and energy that can be harnessed by the organism. This process generally produces CO2, water and a collection of simple nutrients like nitrate or phosphate that can then be taken up by other organisms. The above general form, when considering O2 as the oxidant, is the equation for respiration. In this context specifically, the above equation represents bacterial respiration though the reactants and products are essentially analogous to the short-hand equations used for multi-cellular respiration.

Electron acceptor cascade

Sketch of major electron acceptors in marine sediment porewater based on idealized relative depths Electron Acceptor Cascade in marine sediments.png
Sketch of major electron acceptors in marine sediment porewater based on idealized relative depths

The degradation of organic matter through respiration in the modern ocean is facilitated by different electron acceptors, their favorability based on Gibbs free energy law, and the laws of thermodynamics. [2] This redox chemistry is the basis for life in deep sea sediments and determines the obtainability of energy to organisms that live there. From the water interface moving toward deeper sediments, the order of these acceptors is oxygen, nitrate, manganese, iron, and sulfate. The zonation of these favored acceptors can be seen in Figure 1. Moving downwards from the surface through the zonation of these deep ocean sediments, acceptors are used and depleted. Once depleted the next acceptor of lower favorability takes its place. Thermodynamically, oxygen represents the most favorable electron accepted but is quickly used up in the water sediment interface and O2 concentrations extends only millimeters to centimeters down into the sediment in most locations of the deep sea. This favorability indicates an organism's ability to obtain higher energy from the reaction which helps them compete with other organisms. [3] In the absence of these acceptors, organic matter can also be degraded through methanogenesis, but the net oxidation of this organic matter is not fully represented by this process. Each pathway and the stoichiometry of its reaction are listed in table 1. [3]

Due to this quick depletion of O2 in the surface sediments, a majority of microbes use anaerobic pathways to metabolize other oxides such as manganese, iron, and sulfate. [4] It is also important to figure in bioturbation and the constant mixing of this material which can change the relative importance of each respiration pathway. For the microbial perspective please reference the electron transport chain.

Remineralisation in sediments

Reactions

Relative favorability of reduction reactions in marine sediments based on thermodynamic energetics. Origin of arrows indicate energy associated with half-cell reaction. Length of arrow indicates an estimate of DG for the reaction (Adapted from Libes, 2011). 2Reduction reaction energetics.png
Relative favorability of reduction reactions in marine sediments based on thermodynamic energetics. Origin of arrows indicate energy associated with half-cell reaction. Length of arrow indicates an estimate of ΔG for the reaction (Adapted from Libes, 2011).

A quarter of all organic material that exits the photic zone makes it to the seafloor without being remineralised and 90% of that remaining material is remineralised in sediments itself. [1] Once in the sediment, organic remineralisation may occur through a variety of reactions. [5] The following reactions are the primary ways in which organic matter is remineralised, in them general organic matter (OM) is often represented by the shorthand: (CH2O)106(NH3)16(H3PO4).

Aerobic respiration

Aerobic respiration is the most preferred remineralisation reaction due to its high energy yield. Although oxygen is quickly depleted in the sediments and is generally exhausted centimeters from the sediment-water interface.

Anaerobic respiration

In instances in which the environment is suboxic or anoxic, organisms will prefer to utilize denitrification to remineralise organic matter as it provides the second largest amount of energy. In depths below where denitrification is favored, reactions such as Manganese Reduction, Iron Reduction, Sulfate Reduction, Methane Reduction (also known as Methanogenesis), become favored respectively. This favorability is governed by Gibbs Free Energy (ΔG). In a water body, sediment seabed, or soil, the sorting of these chemical reactions with depth in order of energy provided is called a redox gradient.

Respiration typeReactionΔG
AerobicOxygen reduction-29.9
AnaerobicDenitrification-28.4
Manganese reduction-7.2
Iron reduction-21.0
Sulfate reduction-6.1
Methane fermentation (Methanogenesis)-5.6

Redox zonation

Redox zonation refers to how the processes that transfer terminal electrons as a result of organic matter degradation vary depending on time and space. [6] Certain reactions will be favored over others due to their energy yield as detailed in the energy acceptor cascade detailed above. [7] In oxic conditions, in which oxygen is readily available, aerobic respiration will be favored due to its high energy yield. Once the use of oxygen through respiration exceeds the input of oxygen due to bioturbation and diffusion, the environment will become anoxic and organic matter will be broken down via other means, such as denitrification and manganese reduction. [8]

Remineralisation in the open ocean

Food web showing the flow of carbon in the open ocean Oceanic Food Web.jpg
Food web showing the flow of carbon in the open ocean

In most open ocean ecosystems only a small fraction of organic matter reaches the seafloor. Biological activity in the photic zone of most water bodies tends to recycle material so well that only a small fraction of organic matter ever sinks out of that top photosynthetic layer. Remineralisation within this top layer occurs rapidly and due to the higher concentrations of organisms and the availability of light, those remineralised nutrients are often taken up by autotrophs just as rapidly as they are released.

What fraction does escape varies depending on the location of interest. For example, in the North Sea, values of carbon deposition are ~1% of primary production [9] while that value is <0.5% in the open oceans on average. [10] 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 100–1,200 m (330–3,940 ft) in the water column, decreasing down to about 1,200 m where remineralisation rates remain pretty constant at 0.1 μmol kg−1 yr−1. [11] As a result of this, the pool of remineralised carbon (which generally takes the form of carbon dioxide) tends to increase in the photic zone.

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 [12] while suspended particles and dissolved organics are mostly consumed by remineralisation. [13] This happens in part due to the fact that organisms must typically ingest nutrients smaller than they are, often by orders of magnitude. [14] With the microbial community making up 90% of marine biomass, [15] it is particles smaller than the microbes (on the order of 10−6 [16] ) that will be taken up for remineralisation.

See also

Related Research Articles

<span class="mw-page-title-main">Redox</span> Chemical reaction in which oxidation states of atoms are changed

Redox is a type of chemical reaction in which the oxidation states of substrate change.

<span class="mw-page-title-main">Primary production</span> Synthesis of organic compounds from carbon dioxide by biological organisms

In ecology, primary production is the synthesis of organic compounds from atmospheric or aqueous carbon dioxide. It principally occurs through the process of photosynthesis, which uses light as its source of energy, but it also occurs through chemosynthesis, which uses the oxidation or reduction of inorganic chemical compounds as its source of energy. Almost all life on Earth relies directly or indirectly on primary production. The organisms responsible for primary production are known as primary producers or autotrophs, and form the base of the food chain. In terrestrial ecoregions, these are mainly plants, while in aquatic ecoregions algae predominate in this role. Ecologists distinguish primary production as either net or gross, the former accounting for losses to processes such as cellular respiration, the latter not.

<span class="mw-page-title-main">Biological pump</span> Carbon capture process in oceans

The biological pump, also known as the marine carbon pump, is, in its simplest form, the ocean's biologically driven sequestration of carbon from the atmosphere and land runoff to the ocean interior and seafloor sediments. It is the part of the 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).

<span class="mw-page-title-main">Biogeochemical cycle</span> Chemical transfer pathway between Earths biological and non-biological parts

A biogeochemical cycle is the pathway by which a chemical substance cycles the biotic and the abiotic compartments of Earth. The biotic compartment is the biosphere and the abiotic compartments are the atmosphere, hydrosphere and lithosphere. There are biogeochemical cycles for chemical elements, such as for calcium, carbon, hydrogen, mercury, nitrogen, oxygen, phosphorus, selenium, iron and sulfur, as well as molecular cycles, such as for water and silica. There are also macroscopic cycles, such as the rock cycle, and human-induced cycles for synthetic compounds such as polychlorinated biphenyls (PCBs). In some cycles there are reservoirs where a substance can remain or be sequestered for a long period of time.

<span class="mw-page-title-main">Denitrification</span> Microbially facilitated process

Denitrification is a microbially facilitated process where nitrate (NO3) is reduced and ultimately produces molecular nitrogen (N2) through a series of intermediate gaseous nitrogen oxide products. Facultative anaerobic bacteria perform denitrification as a type of respiration that reduces oxidized forms of nitrogen in response to the oxidation of an electron donor such as organic matter. The preferred nitrogen electron acceptors in order of most to least thermodynamically favorable include nitrate (NO3), nitrite (NO2), nitric oxide (NO), nitrous oxide (N2O) finally resulting in the production of dinitrogen (N2) completing the nitrogen cycle. Denitrifying microbes require a very low oxygen concentration of less than 10%, as well as organic C for energy. Since denitrification can remove NO3, reducing its leaching to groundwater, it can be strategically used to treat sewage or animal residues of high nitrogen content. Denitrification can leak N2O, which is an ozone-depleting substance and a greenhouse gas that can have a considerable influence on global warming.

The pedosphere is the outermost layer of the Earth that is composed of soil and subject to soil formation processes. It exists at the interface of the lithosphere, atmosphere, hydrosphere and biosphere. The pedosphere is the skin of the Earth and only develops when there is a dynamic interaction between the atmosphere, biosphere, lithosphere and the hydrosphere. The pedosphere is the foundation of terrestrial life on Earth.

<span class="mw-page-title-main">Bioturbation</span> Reworking of soils and sediments by organisms.

Bioturbation is defined as the reworking of soils and sediments by animals or plants. It includes burrowing, ingestion, and defecation of sediment grains. Bioturbating activities have a profound effect on the environment and are thought to be a primary driver of biodiversity. The formal study of bioturbation began in the 1800s by Charles Darwin experimenting in his garden. The disruption of aquatic sediments and terrestrial soils through bioturbating activities provides significant ecosystem services. These include the alteration of nutrients in aquatic sediment and overlying water, shelter to other species in the form of burrows in terrestrial and water ecosystems, and soil production on land.

<span class="mw-page-title-main">Sediment–water interface</span> The boundary between bed sediment and the overlying water column

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<span class="mw-page-title-main">Phosphorus cycle</span> Biogeochemical movement

The phosphorus cycle is the biogeochemical cycle that describes the movement of phosphorus through the lithosphere, hydrosphere, and biosphere. Unlike many other biogeochemical cycles, the atmosphere does not play a significant role in the movement of phosphorus, because phosphorus and phosphorus-based compounds are usually solids at the typical ranges of temperature and pressure found on Earth. The production of phosphine gas occurs in only specialized, local conditions. Therefore, the phosphorus cycle should be viewed from whole Earth system and then specifically focused on the cycle in terrestrial and aquatic systems.

<span class="mw-page-title-main">Marine snow</span> Shower of organic detritus in the ocean

In the deep ocean, marine snow is a continuous shower of mostly organic detritus falling from the upper layers of the water column. It is a significant means of exporting energy from the light-rich photic zone to the aphotic zone below, which is referred to as the biological pump. Export production is the amount of organic matter produced in the ocean by primary production that is not recycled (remineralised) before it sinks into the aphotic zone. Because of the role of export production in the ocean's biological pump, it is typically measured in units of carbon. The term was first coined by the explorer William Beebe as he observed it from his bathysphere. As the origin of marine snow lies in activities within the productive photic zone, the prevalence of marine snow changes with seasonal fluctuations in photosynthetic activity and ocean currents. Marine snow can be an important food source for organisms living in the aphotic zone, particularly for organisms which live very deep in the water column.

<span class="mw-page-title-main">Ecosystem respiration</span> The oxidation of organic compounds by organisms in an ecosystem

Ecosystem respiration is the sum of all respiration occurring by the living organisms in a specific ecosystem. The two main processes that contribute to ecosystem respiration are photosynthesis and cellular respiration. Photosynthesis uses carbon-dioxide and water, in the presence of sunlight to produce glucose and oxygen whereas cellular respiration uses glucose and oxygen to produce carbon-dioxide, water, and energy. The coordination of inputs and outputs of these two processes creates a completely interconnected system, constituting the underlying functioning of the ecosystems overall respiration.

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<span class="mw-page-title-main">Redox gradient</span>

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<span class="mw-page-title-main">Benthic-pelagic coupling</span>

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