Promoting the viability of beneficial soil organisms is an element of soil conservation; moreover this includes macroscopic species, notably the earthworm, as well as microorganisms. Positive effects of the earthworm are known well, as to aeration and promotion of macronutrient availability. When worms excrete egesta in the form of casts, a balanced selection of minerals and plant nutrients is made into a form accessible for root uptake. US research shows that earthworm casts are five times richer in available nitrogen, seven times richer in available phosphates and eleven times richer in available potash than the surrounding upper150 mm of soil. The weight of casts produced may be greater than 4.5 kg per worm per year. By burrowing, the earthworm is of value in creating soil porosity, creating channels enhancing the processes of aeration and drainage.

Soil microorganisms play a vital role in macronutrient wildlife. For example, nitrogen fixation is carried out by free-living or symbiotic bacteria. These bacteria have the nitrogenase enzyme that combines gaseous nitrogen with hydrogen to produce ammonia, which is then further converted by the bacteria to make other organic compounds. Some nitrogen fixing bacteria such as rhizobia live in the root nodules of legumes. Here they form a mutualistic relationship with the plant, producing ammonia in exchange for carbohydrates. In the case of the carbon cycle, carbon is transferred within the biosphere as heterotrophs feed on other organisms. This process includes the uptake of dead organic material (detritus) by fungi and bacteria in the form of fermentation or decay phenomena.

Mycorrhizae are symbiotic associations between soil-dwelling fungi and the roots of vascular plants. The mycorrhizal fungi increase the availability of minerals, water, and organic nutrients to the plant, while extracting sugars and amino acids from the plant. There are two main types, endomycorrhizae (which penetrate the roots) and ectomycorrhizae (which resemble 'socks', forming a sheath around the roots). They were discovered when scientists observed that certain seedlings failed to grow or prosper without soil from their native environment.

Some soil microorganisms known as extremophiles have remarkable properties of adaptation to extreme environmental conditions including temperature, pH and water deprivation.

The viability of soil organisms can be compromised when insecticides and herbicides are applied to planting regimes. Often there are unforeseen and unintended consequences of such chemical use in the form of death of impaired functioning of soil organisms. Thus any use of pesticides should only be undertaken after thorough understanding of residual toxicities upon soil organisms as well as terrestrial ecological components.

Killing soil microorganisms is a deleterious impact of slash and burn agricultural methods. With the surface temperatures generated, virtual annilation of soil and vegetative cover organisms are destroyed, and in many environments these effects can be virtually irreversible (at least for generations of mankind). Shifting cultivation is also a farming system that often employs slash and burn as one of its elements.

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