biogeochemistry Biogeochemistry is the scientific discipline that involves the study of the chemical, physical, geological, and biological processes and reactions that govern the composition of the natural environment (including the biosphere, the cryosphere ...

, remineralisation (or remineralization) refers to the breakdown or transformation of

organic matter Organic matter, organic material, or natural organic matter refers to the large source of carbon-based compounds found within natural and engineered, terrestrial, and aquatic environments. It is matter composed of organic compounds that have c ...

(those molecules derived from a biological source) into its simplest

inorganic In chemistry, an inorganic compound is typically a chemical compound that lacks carbon–hydrogen bonds, that is, a compound that is not an organic compound. The study of inorganic compounds is a subfield of chemistry known as ''inorganic chemist ...

forms. These transformations form a crucial link within

ecosystem An ecosystem (or ecological system) consists of all the organisms and the physical environment with which they interact. These biotic and abiotic components are linked together through nutrient cycles and energy flows. Energy enters the syst ...

s as they are responsible for liberating the energy stored in

organic molecules In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen or carbon-carbon bonds. Due to carbon's ability to catenate (form chains with other carbon atoms), millions of organic compounds are known. The s ...

and recycling matter within the system to be reused as

nutrient A nutrient is a substance used by an organism to survive, grow, and reproduce. The requirement for dietary nutrient intake applies to animals, plants, fungi, and protists. Nutrients can be incorporated into cells for metabolic purposes or excre ...

s by other

organism In biology, an organism () is any living system that functions as an individual entity. All organisms are composed of cells ( cell theory). Organisms are classified by taxonomy into groups such as multicellular animals, plants, and fu ...

s. Remineralisation is normally viewed as it relates to the cycling of the major biologically important elements such as

carbon Carbon () is a chemical element with the symbol C and atomic number 6. It is nonmetallic and tetravalent—its atom making four electrons available to form covalent chemical bonds. It belongs to group 14 of the periodic table. Carbon ma ...

nitrogen Nitrogen is the chemical element with the symbol N and atomic number 7. Nitrogen is a nonmetal and the lightest member of group 15 of the periodic table, often called the pnictogens. It is a common element in the universe, estimated at se ...

and

phosphorus Phosphorus is a chemical element with the symbol P and atomic number 15. Elemental phosphorus exists in two major forms, white phosphorus and red phosphorus, but because it is highly reactive, phosphorus is never found as a free element on Ea ...

. 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 Medicine is the science and practice of caring for a patient, managing the diagnosis, prognosis, prevention, treatment, palliation of their injury or disease, and promoting their health. Medicine encompasses a variety of health care practic ...

and

physiological Physiology (; ) is the scientific study of functions and mechanisms in a living system. As a sub-discipline of biology, physiology focuses on how organisms, organ systems, individual organs, cells, and biomolecules carry out the chemica ...

fields, where it describes the development or redevelopment of mineralized structures in organisms such as

teeth A tooth ( : teeth) is a hard, calcified structure found in the jaws (or mouths) of many vertebrates and used to break down food. Some animals, particularly carnivores and omnivores, also use teeth to help with capturing or wounding prey, ...

or bone. In the field of

, 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 Decomposition or rot is the process by which dead organic substances are broken down into simpler organic or inorganic matter such as carbon dioxide, water, simple sugars and mineral salts. The process is a part of the nutrient cycle and ...

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 ithin 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: : + Oxidant -> + \underset + \underset 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 ) into and energy that can be harnessed by the organism. This process generally produces , 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 as the oxidant, is the equation for respiration. In this context specifically, the above equation represents bacterial

respiration Respiration may refer to: Biology * Cellular respiration, the process in which nutrients are converted into useful energy in a cell ** Anaerobic respiration, cellular respiration without oxygen ** Maintenance respiration, the amount of cellul ...

though the reactants and products are essentially analogous to the short-hand equations used for multi-cellular respiration.

Electron acceptor cascade

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 The laws of thermodynamics are a set of scientific laws which define a group of physical quantities, such as temperature, energy, and entropy, that characterize thermodynamic systems in thermodynamic equilibrium. The laws also use various paramet ...

. This

redox Redox (reduction–oxidation, , ) is a type of chemical reaction in which the oxidation states of substrate change. Oxidation is the loss of electrons or an increase in the oxidation state, while reduction is the gain of electrons or ...

chemistry is the basis for life in

deep sea The deep sea is broadly defined as the ocean depth where light begins to fade, at an approximate depth of 200 metres (656 feet) or the point of transition from continental shelves to continental slopes. Conditions within the deep sea are a combin ...

sediment Sediment is a naturally occurring material that is broken down by processes of weathering and erosion, and is subsequently transported by the action of wind, water, or ice or by the force of gravity acting on the particles. For example, sand ...

s 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 Oxygen is the chemical element with the symbol O and atomic number 8. It is a member of the chalcogen group in the periodic table, a highly reactive nonmetal, and an oxidizing agent that readily forms oxides with most elements ...

nitrate Nitrate is a polyatomic ion with the chemical formula . Salts containing this ion are called nitrates. Nitrates are common components of fertilizers and explosives. Almost all inorganic nitrates are soluble in water. An example of an insolu ...

manganese Manganese is a chemical element with the Symbol (chemistry), symbol Mn and atomic number 25. It is a hard, brittle, silvery metal, often found in minerals in combination with iron. Manganese is a transition metal with a multifaceted array of ...

iron Iron () is a chemical element with symbol Fe (from la, ferrum) and atomic number 26. It is a metal that belongs to the first transition series and group 8 of the periodic table. It is, by mass, the most common element on Earth, right in ...

, and

sulfate The sulfate or sulphate ion is a polyatomic anion with the empirical formula . Salts, acid derivatives, and peroxides of sulfate are widely used in industry. Sulfates occur widely in everyday life. Sulfates are salts of sulfuric acid and many ...

. 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 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. 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. Due to this quick depletion of in the surface sediments, a majority of microbes use

anaerobic Anaerobic means "living, active, occurring, or existing in the absence of free oxygen", as opposed to aerobic which means "living, active, or occurring only in the presence of oxygen." Anaerobic may also refer to: * Anaerobic adhesive, a bonding a ...

pathways to metabolize other oxides such as manganese, iron, and sulfate. It is also important to figure in

bioturbation 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 ...

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 An electron transport chain (ETC) is a series of protein complexes and other molecules that transfer electrons from electron donors to electron acceptors via redox reactions (both reduction and oxidation occurring simultaneously) and couples ...

Remineralisation in sediments

Reactions

A quarter of all organic material that exits the

photic zone The photic zone, euphotic zone, epipelagic zone, or sunlight zone is the uppermost layer of a body of water that receives sunlight, allowing phytoplankton to perform photosynthesis. It undergoes a series of physical, chemical, and biological pro ...

makes it to the seafloor without being remineralised and 90% of that remaining material is remineralised in sediments itself. Once in the sediment, organic remineralisation may occur through a variety of reactions. 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: .

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 The term anoxia means a total depletion in the level of oxygen, an extreme form of hypoxia or "low oxygen". The terms anoxia and hypoxia are used in various contexts: * Anoxic waters, sea water, fresh water or groundwater that are depleted of diss ...

, organisms will prefer to utilize

denitrification 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 denit ...

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 Methanogenesis or biomethanation is the formation of methane coupled to energy conservation by microbes known as methanogens. Organisms capable of producing methane for energy conservation have been identified only from the domain Archaea, a group ...

), become favored respectively. This favorability is governed by

Gibbs Free Energy In thermodynamics, the Gibbs free energy (or Gibbs energy; symbol G) is a thermodynamic potential that can be used to calculate the maximum amount of work that may be performed by a thermodynamically closed system at constant temperature an ...

(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.

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. Certain reactions will be favored over others due to their energy yield as detailed in the energy acceptor cascade detailed above. 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.

Remineralisation 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 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.

Heterotroph A heterotroph (; ) is an organism that cannot produce its own food, instead taking nutrition from other sources of organic carbon, mainly plant or animal matter. In the food chain, heterotrophs are primary, secondary and tertiary consumers, but ...

ic organisms will utilize the materials produced by the

autotroph An autotroph or primary producer is an organism that produces complex organic compounds (such as carbohydrates, fats, and proteins) using carbon from simple substances such as carbon dioxide,Morris, J. et al. (2019). "Biology: How Life Wo ...

ic (and

chemotroph A Chemotroph is an organism that obtains energy by the oxidation of electron donors in their environments. These molecules can be organic (chemoorganotrophs) or inorganic ( chemolithotrophs). The chemotroph designation is in contrast to phototr ...

ic) 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 1,200 m where remineralisation rates remain pretty constant at 0.1 μmol kg⁻¹ yr⁻¹. 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 Dissolved organic carbon (DOC) is the fraction of organic carbon operationally defined as that which can pass through a filter with a pore size typically between 0.22 and 0.7 micrometers. The fraction remaining on the filter is called partic ...

(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.

References

{{reflist Biogeochemistry Oceanography Limnology