The complex physical and chemical nature of the soil, its porous structure, immense surface area, and fluctuating supply of organic materials, food, water and chemicals is part of the reason why so many animal, plant and microbial worlds can co-exist simultaneously and find appropriate niches for their development. This provides a range of habitats for a multitude of fauna and flora ranging from macro- to micro- levels depending on climate, vegetation and physical and chemical characteristics of the given soil. The species numbers, composition and diversity of a given soil depends on many factors including aeration, temperature, acidity, moisture, nutrient content and organic substrate.

Soil biodiversity tends to be greater in forests compared to grasslands and in undisturbed natural lands compared to cultivated fields. However the number and types of organisms vary from one system and environment to another and this is strongly influenced by agricultural practices. It is recognised that soil biodiversity therefore can be used as an indicator of soil quality and stable ecosystems.

Soil organisms incorporate plant and animal residues and wastes into the soil and digest them, creating soil humus, the organic constituent so vital to good physical and chemical soil conditions, and recycling carbon and mineral nutrients. This decomposition process includes the release of CO2 to the atmosphere where it can be recycled through higher plants and the release of essential plant nutrients in inorganic forms that can be absorbed by plant roots or leached from the soil. All soil organisms have important effects not only on soil properties but also on the functioning of the ecosystem.