The soil is viewed as an essential part of the process. Microorganisms in the soil feed on the soil organic matter and make the inorganic part available to plants. The fertility of the soil is maintained by returning nutrients removed by the plant in the form of compost and manure and by a system of crop rotation in which crops which remove more nutrients alternate with crops such as legumes which remove less and add some. There are clear differences between the two systems of agriculture in philosophy, sustainability, effect on the environment and wildlife, and amount and type of pollution they generate. But neither system is precisely defined and clear-cut in its practices.
Some conventional farmers use compost and manure and crop rotations.
All are affected by the soil type and climate of their region. There may or may not be differences in the varieties they choose to grow. Even when all these variables are carefully controlled, the studies either demonstrate no differences in nutrient levels or give inconsistent and unreproducible results. It is extremely difficult to rule out all the possible environmental and genetic factors which might influence nutrient content. Many research studies on organic food do not manage to achieve controlled conditions, in which case it's impossible to say what might have caused any difference which is revealed.