Remineralisation

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 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:

${\displaystyle \text{Organic}\text{Matter}+\text{Oxidant}⟶\text{Liberated}\text{Simple}\text{Nutrients}+\underset{\text{Carbon}\text{Dioxide}}{{\text{CO}}_2^{}}+\underset{\text{Water}}{{\text{H}}_2^{}\text{O}}}$

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

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. 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 acceptor 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. 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 O₂ in the surface sediments, a majority of microbes use anaerobic pathways to metabolize other oxides such as manganese, iron, and sulfate. 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.