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Major classes of organic matter include carbohydrates, proteins and amino acids, lipids, lignin, and tannins. The reactivity (or “quality”) of organic carbon varies as a function of factors including its elemental stoichiometry, bond structure, and the degree of oxidation (e.g., NOSC or C_ox). For example, lignin and tannins are phenolic compounds that contain aromatic ring structures that are difficult to cleave. Proteins and amino acids are rich in nitrogen whereas carbohydrates lack nitrogen entirely. Carbohydrates range from simple sugars (e.g., glucose) to large polysaccharides (e.g., cellulose, hemicellulose). Lipids are partially or completely hydrophobic and can have linear, branching, and ring structures.

Table 3.3 Nominal oxidation state of carbon for major classes of organic matter

Compound	NOSC
CO2	+ 4
tannins	+ 0.64
carbohydrates	+ 0.03
lignin	– 0.27
protein	– 0.82
lipids	– 1.34
CH4	– 4

Average NOSC values for organic matter in sulfidic floodplain sediments are from Figure S4 in Boye et al. (2017). The NOSC values for other systems and sites will vary depending on the identity of the specific molecules that make up each broad class of organic matter. Values for CO₂ and CH₄ were calculated following LaRowe and Van Cappellen (2011).

These compound classes differ in their potential thermodynamic energy yield, as indicated by their NOSC (Table 3.3). The degree of organic matter oxidation and the physicochemical environment control which molecules are energetically available for microbial degradation and which are preserved (Boye et al., 2017; Pracht et al., 2018). Even molecules with a high potential energy yield can be preserved if they contain bonds that are difficult to cleave (e.g., those in phenolic rings) or if environmental conditions inhibit the activities of extracellular enzymes of the microbial decomposer consortium. This helps explain why, for example, there can be high concentrations of tannins in wetlands and surrounding “blackwater” aquatic systems, even though tannins have the highest NOSC of the major compound classes (Table 3.3). Similarly, the persistence of tropical peats despite warm temperatures is related to high concentrations of aromatic compounds (including phenolics) in low latitude peatlands (Hodgkins et al., 2018).

As organic carbon undergoes decomposition in wetlands, different molecules are preferentially mineralized or preserved, leading to changes in the composition of soil organic matter. The carbon in leaves, stems, and roots of herbaceous plants is more oxidized (higher NOSC) than that in woody plants, which is consistent with higher rates of decay of non‐woody biomass (Randerson et al., 2006). Leaves with higher lignin concentrations decay more slowly than those with less lignin (Day, 1982; J. Hines et al., 2014). During decomposition, cellulose and hemicellulose decay faster than does lignin, as would be predicted by their NOSC values, and leads to changes in organic matter chemistry over time in both litter and soil (Baldock et al., 2004; Benner et al., 1987; Worrall et al., 2017).

The transformation of organic compounds during the decomposition process creates a large pool of soil organic matter of altered reactivity in a process called humification. There is debate as to whether humification generates an amalgamation of small, poorly characterized compounds (Sutton & Sposito, 2005), the synthesis of complex macromolecules with a higher molecular weight than the starting compounds (De Nobili et al., 2020), or if the entire idea of humification should be abandoned entirely (Lehmann & Kleber, 2015). Regardless, it is clear that the chemistry of soil organic matter does change during decomposition. For example, organic matter in deeper peats from bogs, fens, and swamps was more decomposed and less oxidized (lower NOSC) than surface peat, with most of the change happening within the top 50 cm (roughly the last 200 years) (T. R. Moore et al., 2018).