Organic matter is degraded (mineralized) in sediments by an array of aerobic and anaerobic microbial processes with a concurrent release of inorganic nutrients. The rates of decay depend on a variety of factors such as, organic matter quality (i.e., the content of protein, cellulose, lignin, etc.), age (decomposition stage) and temperature (season). The chemical composition of organic matter can be generalized according to: (CH2O)x(NH3)y(H3PO4)z, where x, y and z vary depending on the origin and age of the material. For marine organic matter (e.g. phytoplankton) having the Redfield composition the stoichiometry is as follows: x = 106, y = 16, and z = 1.
Almost all heterotrophic organisms with aerobic metabolism have the enzymatic capacity to perform a total oxidation of organic carbon. Organic matter may therefore be completely metabolized by a single organism to H2O, CO2 and inorganic nutrients using oxygen as electron acceptor according to eqn. (1):
(CH2O)x(NH3)y(H3PO4)z + xO2 → xCO2 + yNH3 + zH3PO4 + xH2O (1)
However, due to an efficient energy metabolism, a large fraction of the metabolized organic matter ends up as cell material. Aerobic decomposition is unique in the sense that oxygen-containing radicals such as superoxide anion (O2 -), hydrogen peroxide (H2O2) and hydroxyl radicals (.OH) are readily formed and consumed. These are capable of breaking strong chemical bonds and thus depolymerize relatively refractory organic compounds rich in aromatic structures like lignin.
As the oxic (oxygen containing) zone in coastal sediments usually is limited to an uppermost mm thick layer, much of deposited organic carbon is buried in a more or less degraded form into anoxic layers (Fig. 8). Here mutualistic consortia of bacteria accomplish anaerobic decomposition because no single type of anaerobic bacterium seems capable of complete mineralization. Anaerobic bacteria also appear more limited than aerobic organisms in their ability to depolymerize certain large complex molecules. These include among others saturated hydrocarbons, certain pigments and lignin.
Anaerobic decomposition occurs stepwise, involving several different functional types of bacteria. First, large and normally complex polymeric organic molecules are stepwise split into water-soluble monomers (amino acids, monosaccharides and fatty acids) by hydrolysis and fermentation under the production of energy and release of inorganic nutrients, e.g. mixed propionate and acetate formation (eqn. (2)):
6(CH2O)x(NH3)y(H3PO4)z → xCH3CH2COOH + xCH3COOH + xCO2 + xH2 + 6yNH3 + 6zH3PO4 (2)
These small organic acids are then oxidized completely to H2O and CO2 by a number of respiring microorganisms using a variety of oxidized inorganic compounds as electron acceptors.
The individual anaerobic respiration processes generally occur in a sequence with depth in the sediment according to the availability of electron acceptors: Mn4+, NO3-, Fe3+, SO42-and CO2 respiration. The actual sequence is determined by the ability of each electron acceptor to receive electrons, and thus the energy output per degraded organic carbon atom, e.g. manganese respiration is energetically more favourable than sulfate reduction. The suboxic zone contains the most potent anaerobic electron acceptors, Mn4+, NO3-, and Fe3+. The transition from one electron acceptor to the other downwards in the sediment occurs when the most favourable is exhausted, although some vertical overlap may occur. Two representative examples of anaerobic degradation stoichiometries are manganese and sulfate reduction (eqn. (3) and (4)):
CH3COOH + 4MnO2 + 8H+ → 4Mn2+ + 2CO2 + 6H2O (3)
CH3COOH + SO42- → 2CO2 + S2- + 2H2O (4)
A significant portion of sediment oxygen uptake is not caused by aerobic respiration, but is rather due to reoxidation of reduced inorganic metabolites (e.g., NH4+, Mn2+, Fe2+ and H2S) close to the oxic/anoxic interface. Thus, up to 85% of the sulfide produced by sulfate reduction is not trapped permanently by reactions with iron and other metals, but is continuously diffusing upwards to be reoxidized in the near-surface sediment. About 50% or more of the total sediment oxygen uptake is usually consumed directly or indirectly by oxidation of sulfide. Reoxidation can be a pure chemical process, but it is usually mediated by chemoautotrophic microorganisms.
The strict vertical distribution of electron acceptors, as mentioned above, is an over-simplification of the true spatial distribution. The influence of sediment inhomogeneities, such as worm burrows, on porewater profiles and vertical distribution of microbial processes has been clearly documented. Furthermore, patches associated with, e.g., faecal pellets may create anaerobic microniches, where anaerobic processes, such as denitrification and sulfate reduction, occur in otherwise oxic surface sediments.[39,40]
Nevertheless, the usually observed decreasing degradation rate with depth in sediments is not solely caused by the less efficient electron acceptors in the deeper layers, but rather by decreasing degradability of organic matter.