Soil is an integral compartment of the environment and the central organizer of the terrestrial ecosystem. Soil quality is the fundamental foundation of environmental quality. Indiscriminate use of agro-chemicals, excessive and deep tillage, and luxury irrigation have degraded soils, particularly in semi-arid Mediterranean areas, as well as polluted surface and ground waters, and contaminated air. Understanding the role of soil organic matter and biodiversity in agricultural ecosystems has highlighted the value and importance of a range of processes that maintain and fulfil human needs. Numerous microorganisms, especially those associated with roots, have the ability to increase plant growth and productivity. Application of organic manure and conservation tillage could lead to the reduction in chemical fertilizers usage, improvement soil biological structure and reduction of soil & water contamination.