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Concerns for soil carbon stocks with increasing global temperature have recently been raised. Adopting a multidisciplinary, reductionist approach and investigating the degradation and turnover of individual compound classes is essential in order to gain a greater knowledge of soil carbon dynamics and address the issue of soils becoming sources of carbon dioxide rather than sinks. The second most abundant natural biopolymer on earth is lignin and therefore its contribution to soil organic matter (SOM) is significant. The physical recalcitrance of lignin, together with its stability in laboratory studies has led many to assume that its degradation in soils must be slow. However, recent findings suggest that it is more easily degraded than conventionally perceived. This thesis investigates the molecular mechanisms involved in the degradation and turnover of lignin in the model system and the natural environment, linking together the associated biological and geochemical changes. White rot fungi are the primary degraders of lignin, secreting a complex array of extracellular enzymes that result in an oxidative attack of the biopolymer. Laboratory based, time-dependent growth experiments were performed and investigated the key enzymatic changes associated with lignin breakdown by the white rot fungus Pleurotus ostreatus cultivated on wheat straw (Triticum aestivum [L.]), ash (Fraxinus excelsior [L]) and Sitka spruce (Picea sitchensis [Bong.] Carr). The corresponding geochemical changes to lignin structure were also analysed using on- line thermally assisted hydrolysis and methylation (THM) in the presence of tetramethylammonium hydroxide (TMAH). Fungal growth, enzyme activity and lignin breakdown were substrate dependent, with higher levels of enzyme activity, lignin oxidation and side chain cleavage in the angiosperm (wheat straw and ash) systems than the gymnosperm (Sitka spruce) system. Early peaks in manganese dependent peroxidase and laccase activity were followed by a more gradual increase in lignin oxidation and side chain cleavage. On-line thermally assisted hydrolysis and methylation (THM) in the presence of 13C_ labelled/unlabelled tetramethylammonium hydroxide (TMAH) was used to investigate the phenolic distributions and their quantitative changes in soils beneath a Sitka spruce afforested moorland, an unforested moorland and an unimproved lowland grassland. \3C-labelled TMAH was successfully employed to distinguish between lignin- and non-lignin- derived (particularly tannin) phenols. Afforestation had a significant effect on phenolic degradation dynamics in these peaty gley soils. The Sitka spruce afforested moorland recorded a change in input and land preparation either as a result of changing vegetation input or due to land preparation prior to planting. Changes to soil carbon stocks were also investigated in these three soils and afforestation appeared to result in the accumulation of organic carbon in mineral horizons.