This concerns soil properties related to the microbial and faunal activity in soil. These organisms include earthworms, nematodes, protozoa, fungi, bacteria and different arthropods. Soil biology plays a vital role in determining many soil characteristics, yet, being a relatively new science, much remains unknown about soil biology and about how the nature of soil is affected. Soil organisms break down organic matter and while doing so make nutrients available for uptake by plants. The nutrients stored in the bodies of soil organisms prevent nutrient loss by leaching. Microbes also maintain soil structure while earthworms are important in bio-turbation in the soil. Bacteria play a vital role in the Nitrogen cycle affecting :

• Mineralization is defined as impregnation with ammonia or a compound of ammonia. It is the process in which pure forms of nitrogen are converted to ammonium by decomposers or bacteria. When a plant or animal dies, or an animal expels waste, the initial form of nitrogen is organic. Bacteria, or fungi in some cases, convert the organic nitrogen within the remains back into ammonium (NH₄⁺), a process called ammonification or mineralization.

• Nitrification where bacteria are able to transform nitrogen in the form of ammonium, which is produced by the decomposition of proteins, into nitrates, which are available to growing plants.

• Nitrogen fixation is carried out by free-living nitrogen-fixing bacteria in the soil or water such as Azotobacter, or by those that live in close symbiosis with leguminous plants, such as rhizobia. These bacteria form colonies in nodules they create on the roots of peas, beans, and related species. These are able to convert nitrogen from the atmosphere into nitrogen-containing organic substances.

• Denitrification returns nitrogen to the atmosphere. Denitrifying bacteria tend to be anaerobes, including Achromobacter and Pseudomonas. The purification process caused by oxygen-free conditions converts nitrates and nitrites in soil into nitrogen gas or into gaseous compounds such as nitrous oxide or nitric oxide. In excess, denitrification can lead to overall losses of available soil nitrogen and subsequent loss of soil fertility.

The carbon cycle diagram shows the process by which the element carbon is exchanged between the biosphere, pedosphere, geosphere, hydrosphere, and atmosphere of Earth. This is the most important process on the planet because it allows Earth to recycle and reuse its most abundant element. The annual movements of carbon, the carbon exchanges between reservoirs, occur because of various chemical, physical, geological, and biological processes in the soil.

The microbes living within the soil recycle nutrients such as carbon and nitrogen through the soil system. Much of the organic material added to the litter (the accumulated material at the surface of the soil) or within the root zone each year is almost completely consumed by microbes.Consequently, there is a reservoir of carbon with a very fast turnover time of about1 to 3 years in many cases. The by-products of this microbial consumption are CO₂, H₂O, and a variety of other compounds, collectively known as humus. Humus is less palatable for microbes and is therefore not decomposed very quickly. After it is produced at shallow levels within the soil, part of it may move downward as a clay-humus complex. In the lower parts of the soil it tends to be less oxygen availability and this lack of oxygen makes it even more difficult for microbes to work on this humus and decompose it further. Eventually, due to various processes that stir the soil, this humus moves back up to where there is more oxygen and then the microbes will eventually destroy the humus and release some more CO₂. This humus then constitutes another, longer-lived reservoir of carbon in the soil with ages of several hundred to a thousand years old. Taken together, the fast decomposition and the slower decomposition of humus, both driven by microbial processes, lead to an average residence time of around 20 to 30 years for most soils. The soil microbes (considered in terms of their respiratory output) are very sensitive to the organic carbon content of the soil as well as to the temperature and water content, they respire faster at higher carbon concentrations, higher temperatures and in moister conditions.