On an annual basis, the concept of primary production limitation by soil nutrient in natural systems is complex because of the very strong link between nutrient availability and plant cover spatial structure and species composition. In old and stable ecosystems, the plant community is probably highly adapted to the level of available nutrients. The latter is itself strongly dependent on plant community structure, and it is not obvious that annual primary production is controlled by the flux of nutrients originating from soil humus mineralization. The spatial pattern of the distribution of mineral nutrients in soil is rarely homogenous: nutrient concentrations vary rapidly at different scales, from meter (presence or absence of trees for example) to micrometer (presence or absence of bacteria). Soil fauna distribution and activity, which modify the physical and chemical environment of micro-organisms, are key factors controlling the soil organic nitrogen storage and mineral nitrogen production. The ability of plants to uptake nutrients is another key factor controlling primary productivity and, in a sense, the real soil fertility is also a function of plant distribution and plant underground architecture. This impact of soil biological characteristics on soil fertility can explain the discrepancy sometimes observed between high productivity and low mineral nutrients content, as in Lamto.