lipids
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).
Nutrient availability.
The carbon:nutrient ratio of plants is generally larger than that of soil bacteria and fungi, indicating an imbalance between the supply and demand for nutrients during decomposition (Hessen et al., 2004; Sterner & Elser, 2002). Indeed, litter decomposition studies often show an increase in nutrient concentrations over time, reflecting microbial immobilization of nutrients from the environment (e.g., Conner & Day, 1991). Litter decomposition is sensitive to nutrient availability in plant litter (Enríquez et al., 1993; Webster & Benfield, 1986) and/or the environment (Rejmánková & Houdková, 2006; Song et al., 2011). The degradation of plant litter can be limited by nitrogen availability, as indicated by negative correlations between litter C:N ratios and rates of decomposition (Keuskamp et al., 2015; Lee & Bukaveckas, 2002; Neely & Davis, 1985; Song et al., 2011). A similar pattern is seen with phosphorus (P), where higher litter phosphorus levels can lead to higher decomposition rates (J. Hines et al., 2014). The decomposition of leaf litter is generally limited by phosphorus when leaf N:P ratios are high and by nitrogen when leaf N:P ratios are low. Although there is not a universal N:P ratio that determines when the limiting nutrient changes (Güsewell & Freeman, 2005; Güsewell & Verhoeven, 2006), plants growing in organic wetland soils are more likely to be limited by phosphorus whereas plants in mineral substrates often are limited by nitrogen availability (Bedford et al., 1999). There can be interactions between nutrient availability and carbon quality, with higher nutrient levels stimulating decomposition to a greater degree when leaf litter is of higher quality (i.e., lower lignin content) (Hobbie, 2000). Alternately, the effects of low carbon quality may limit decomposition regardless of nutrient availability (Bridgham & Richardson, 2003).
Physicochemical Inhibition of Decomposition.
Physicochemical inhibition preserves carbon through physical or chemical interferences with microbial decomposition processes. We define inhibitory factors as those that prevent mineralization from proceeding at the potential rate set by the free energy yield of the dominant redox couples. We treat inhibition as a distinct category but acknowledge that it interacts strongly with mechanisms that operate through the redox environment (i.e., O2 availability) and the chemical composition of organic matter.
Phenolic inhibition.
Phenolic compounds can accumulate and inhibit decomposition under conditions that limit the activity of phenol oxidase, the enzyme that degrades phenolics. Because phenol oxidase requires O2 to function, its activity generally is low in fully anaerobic soils, increases in surface soils, and is greatest in aerobic surface litter (Wright & Reddy, 2001). Although other extracellular enzymes involved in carbon mineralization exhibit low activities at lower O2 concentrations (Freeman, Ostle et al., 2004; McLatchey & Reddy, 1998), this is probably not a direct effect of O2 since hydrolytic enzymes do not require O2 to function. Instead, low O2 concentrations result in low phenol oxidase activity, allowing phenolic compounds to accumulate and inhibit hydrolytic enzymes (Fig. 3.3) (Fenner & Freeman, 2011; Freeman, Ostle et al., 2001). So, the O2‐related inhibition of phenol oxidase activity does not just affect the decomposition of lignin and other phenolic compounds, it inhibits the breakdown of multiple classes of organic carbon and acts as an “enzymic latch” that preserves large quantities of carbon in organic wetland soils (Freeman, Ostle et al., 2001). The activity of phenol oxidase is also inhibited by moisture limitation, which may help limit carbon mineralization during droughts when soil O2 concentrations increase (H. Wang et al., 2015).
The enzymic latch mechanism may be most important in wetlands with lignin‐poor vegetation (e.g., those dominated by Sphagnum mosses) and/or those with low soil iron contents (Y. Wang et al., 2017). Although phenol oxidase activity increases in some wetlands with water table drawdown (that is, increased O2 penetration into the soil), this is not a universal response. Instead of being restricted by low soil O2, the activities of phenol oxidase and hydrolytic enzymes can be enhanced in the presence of Fe2+ (Van Bodegom et al., 2005; Hall & Silver, 2013; Liu et al., 2014) and, therefore, may decline following a sustained water table drawdown (Y. Wang et al., 2017). This “iron gate” mechanism differs from the enzymic latch and suggests that increasing soil oxidation in mineral soil wetlands may help protect against the decomposition of lignin (Y. Wang et al., 2017).
Figure 3.3 Effects of O2 availability on enzyme activity and organic matter decomposition. A cascade starts when increased O2 supply stimulates microbial aerobic respiration (A), triggering increased phenol oxidase synthesis