Natural ecosystems sustain soil fertility by an internal nutrient cycling. Climatic events are constraining the microfloral and faunal activities. From monocultured agricultural rotation systems, in contrast, large plantal portions are removed through harvesting and this nutrient removal differentiate them from natural successions. Farmers approach to compensate the removed nutrients by spreading mineral fertilizers, biotechnologically pretreated composts, sewage sludge, animal manures, and animal slurries (chapter 4 in this volume). These returned organic material added to the remaining plant residues differs in its chemical composition, and thus in its availability and biodegradability. Furthermore, agricultural soils are often treated with pesticides and are mechanically treated by ploughing, harrowing, or condensed by heavy machines. Agroecosystems, since several hundreds years under cultivation, seem, despite all these perturbations, enabled to cope with all these constraints. Biomass productions as high as those of natural ecosystem successions are documenting this (chapter 18 in this volume). Nevertheless the soil carbon content can decrease due to inappropriate land use and soil mismanagement practices, causing a decline in soil quality and a loss of C into the atmosphere (e.g., Blair [1], Lal [2], Wu et al. [3]).