Major pathways for humification showing C inputs and the types of condensation reactions that are likely to occur. Pathways are (a) sugar-amine, (b) polyphenol-quinone, (c) lig- nin-quinone, and (d) modified- lignin (after Stevenson 1994, p. 189). 

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... the second stage of (bio)chemical alteration, new compounds form from some of the molecules released during the decomposition stage. These compounds are condensates of a variety of different “ monomers ” and, as a consequence, do not have well-defined composition or structure. Indeed, there is increasing evidence to suggest that the condensates may consist of dynamic clusters of chemically altered and unaltered compounds held together loosely by hydrophobic interactions and hydrogen bonding (Sutton and Sposito 2005). In general, the condensates have higher aromatic character and oxygen content than the average biomass present in soils (Hayes and Malcolm 2001). When compared to plant litter, the condensates have higher levels of carboxylic and fatty-acid C and lower levels of polysaccharide C (Chefez et al. 2002; Zech et al. 1997). Their most important attribute, however, is that they are more recalcitrant to decomposition, either as a result of their intrinsic biochemical properties or enhanced sorption affinities. As shown in Fig. 1, consensus has emerged among researchers that the chemically altered fraction of the condensates are formed by the reactions of amino compounds (acids and sugars) with quinones or reducing sugars to form melanin-type compounds (Flaig 1975; Haider et al. 1975; Hedges 1988; Kononova 1961; Maillard 1916; Martin and Haider 1971; Martin et al. 1975; Stevenson 1994; Tan 2003; Waksman 1932). The amino compounds and reducing sugars are readily available from the lysing of microorganisms, whereas the quinones are the result of oxidation of polyphenols derived from lignin and other plant materials as well as from microorganisms. The condensation of reducing sugars with amino compounds proceeds spontaneously but slowly at typical soil temperatures, and is greatly enhanced by repeated wetting and drying cycles. Many investigators, however, consider the quinone/amino-compound condensation reaction to be the dominant humification pathway in soils (Stevenson 1994). The rate- determining step for this reaction is believed to be the oxidation of the polyphenol to form the quinone. The reaction is faster at high pH, and at the near-neutral pH of most soils assistance from a catalyst is needed for the reaction to proceed at a measurable rate. Biological catalysts include polyphenol oxidase, peroxidase, and laccase enzymes produced by fungi, which mediate the electron transfer from the polyphenol to molecular oxygen (Sjoblad and Bollag 1981, Tate 1992). Other substances in soils either catalyze the reaction – e.g., amorphous silica, charcoal, iron-sorbed smectite (Amonette et al. 2003a, b, 2004; Booth et al. 2004) – or serve as oxidants – e.g., oxides and hydroxides of manganese and iron, smectites (Amonette et al. 2000; Naidja et al. 1998; Shindo and Huang 1984; Wang and Huang 2005). Recent evidence suggests the overall reaction rate increases synergistically when both biological and inorganic catalysts are present (Amonette et al. 2000, 2003a, b). Ultimately, the availability of molecular oxygen determines whether the polyphenol oxidation reaction occurs, as this species also oxidizes the metal oxides and phyllosilicates. Indeed, insufficient oxygen is likely to stop the quinone/amino-compound condensation reaction from occurring in soils, just as it prevents the enzymatic decomposition of peat bogs (Freeman et al. 2001). Too much oxygen, however, and the monomers and newly formed condensates will continue to be altered until their C is fully oxidized to CO . In contrast to the oxidation step, the subsequent condensation reaction with the amine group occurs spontaneously, although many factors (primarily pH) can affect its rate. The mineral phases in soils can have an important impact on (bio)chemical alteration, principally as catalysts of condensation and as oxidants. The dominant minerals in soils on a mass basis are typically quartz and the feldspars, but these minerals have very low specific surfaces (ca. 0.1 m 2 g − 1 ) and correspondingly low impact on chemical alterations of soil organic matter. Minerals with high specific surfaces (>10 m 2 g − 1 ) and high chemical impact on alterations include the phyllosilicate clays, allophanes, and the oxides and hydroxides of manganese and iron. The phyllosilicate clays can be grouped according to whether they are swelling (e.g., smectites, vermiculites) or non-swelling (e.g., kaolinite, illite), with swelling clays offering internal surfaces as high as several hundred square meters per gram. Although some studies have shown correlations between clay content (or clay plus silt) and the amount of soil organic matter (e.g., Six et al. 2002a, b), the surface reactivity and specific surface of soil minerals appear to be better predictors of SOC (Baldock and Skjemstad 2000). Protection of (bio)chemically altered soil organic matter from further microbial decomposition or oxidation by molecular oxygen and extracellular enzymes is essential to significantly lengthen the residence time of C in soils. For protection of new C to occur, some change in the arrangement between this C and other soil particles must occur. Rearrangement can occur in a number of ways but the end state generally involves chemical or physical sorption of the new C to an existing surface coupled with some sort of physical barrier to prevent further access by agents that would decompose or oxidize the C. If not already at a surface, the new C may diffuse or advect to a surface where it can be adsorbed. Alternatively, the soil particles may change position to become reoriented in association with SOC as a result of advection, the mechanical actions of plant and fungal growth, bioturbation by earthworms and other soil fauna, or changes in hydration ...