Soils correspond to the surface layer of the Earth's crust (lithosphere). They develop as a result of the weathering of geological rock formations. They consist of mineral particles derived from the eroded rocks and of organic matter derived from the remains of plants, animals, and microorganisms. Mineral and organic particles are intimately mixed in soil, forming various types of soil aggregates, and are found in association with air (i.e. the soil atmosphere) and an aqueous phase (i.e. the soil solution) in the pores existing between particles and/or aggregates.

The soil represents a favourable habitat for microorganisms and is inhabited by a wide range of microorganisms, including bacteria, fungi, algae, viruses and protozoa. Microorganisms are found in large numbers in soil - usually between one and ten million microorganisms are present per gram of soil - with bacteria and fungi being the most prevalent. However, the availability of nutrients is often limiting for microbial growth in soil and most soil microorganisms may not be physiologically active in the soil at a given time.

Soil microorganisms are very important as almost every chemical transformation taking place in soil involves active contributions from soil microorganisms. In particular, they play an active role in soil fertility as a result of their involvement in the cycle of nutrients like carbon and nitrogen, which are required for plant growth. For example, soil microorganisms are responsible for the decomposition of the organic matter entering the soil (e.g. plant litter) and therefore in the recycling of nutrients in soil. Certain soil microorganisms such as mycorrhizal fungi can also increase the availability of mineral nutrients (e.g. phosphorus) to plants. Other soil microorganisms can increase the amount of nutrients present in the soil. For instance, nitrogen-fixing bacteria can transform nitrogen gas present in the soil atmosphere into soluble nitrogenous compounds that plant roots can utilise for growth. These microorganisms, which improve the fertility status of the soil and contribute to plant growth, have been termed 'biofertilizers' and are receiving increased attention for use as microbial inoculants in agriculture. Similarly, other soil microorganisms have been found to produce compounds (such as vitamins and plant hormones) that can improve plant health and contribute to higher crop yield. These microorganisms (called 'phytostimulators') are currently studied for possible use as microbial inoculants to improve crop yield.

In contrast to these beneficial soil microorganisms, other soil microorganisms are pathogenic to plants and may cause considerable damage to crops. Large numbers of pathogenic microorganisms are routinely found in the soil and many of them can infect the plant through the roots. However, certain native microorganisms present in the soil are antagonistic to these pathogens and can prevent the infection of crop plants. Antagonism against plant pathogens usually involves competition for nutrients and/or production of inhibitory compounds such as secondary metabolites (antimicrobial metabolites and antibiotics) and extracellular enzymes. Other soil microorganisms produce compounds that stimulate the natural defence mechanisms of the plant and improve its resistance to pathogens. Collectively, these soil microorganisms have been termed 'biopesticides' and represent an emerging and important alternative (i.e. biological control) to the use of chemical pesticides for the protection of crops against certain pathogens and pests.