Soil biology is a branch of science that focuses on the organisms living in or interacting with the soil. These organisms can be microorganisms such as bacteria or fungi, or macroorganisms such as plants and animals. 

Their activities instigate physical, chemical, and biological processes that take place above and below ground. In the long run, these organisms and their interactions shape the soil characteristics, which influence its ecosystem and the location where it is found. 

As a science, soil biology involves the study of the ecological food web that takes place due to the interaction of these living organisms. 

And since the ground serves as the interaction site for various organisms on earth, it also investigates the impact of their activities and their interactions on its properties and formation.

What is Soil?

Soil originated from the disintegration of rocks in the pedosphere, the uppermost layer of Earth’s surface not occupied by water. 

Natural rocks and those in man-made structures disintegrate when they are exposed to weathering agents such as water, wind, frost, temperature shifts, and other atmospheric gasses.

Soil Components

Despite having similar components, the ratio of each component in soils differs from one area to another. These differences arise from:

  • soil-forming factors, which are the parent materials in soil formation
  • climate and topology of the site of soil formation
  • the organisms living above and below ground
  • human influences, and 
  • the extent of the time these factors have been interacting.[1,2]   

Hence, soil characteristics not only differ based on location but also when and how it is formed. And these components are broadly organized into four groups:[1]   

1. Minerals

Minerals are crystalline solids that aggregate to form a rock. Disintegrated rocks result in mineral particles of different sizes and species, which aggregate to form soil. 

Minerals constitute about 45% of the overall components. They are often found as mineral salts, and most are acidic if dissolved. Common minerals found in soil include silicon dioxide, aluminum silicates, oxides of iron, and calcium carbonate.

2. Soil Organic Matter

Soil organic matter, or SOM, is decomposing dead plants and animals that can be transformed into humus, a dark, nutrient-rich, complex organic matter.[2]    

Bacteria, fungi, and small animals such as mites, millipedes, earthworms, slugs, and shelled snails feed on dead plants and larger animals, breaking down complex molecules such as lignin, cellulose, lipids and proteins in the process. 

Subsequently, these complex molecules are decomposed into simpler molecules, providing plants and other photosynthetic microbes with carbon and nutrients they can use to produce food for other animals.

3. Water

Water fills the pore spaces between mineral and SOM particles or it’s absorbed onto the surface of these particles. 

4. Air

Air fills the open pore spaces that are not occupied by water. It is used by organisms that live underground for their respiration

Soil Profile

A soil’s uniqueness is reflected in its properties, which are recorded chronologically in layers, called horizons. These horizons are vertically combined to form a soil profile.  

Properties of Horizons

Each horizon differs in its thickness and can be characterized based on various physical and chemical properties of the ground. 

Notable properties include:[2]  

  • Color, which results from the proportion of each component. For example, the types of minerals found in the dirt, the proportion of SOM, and water.  
  • Soil structure or ped describes the aggregation of soil particles. It is classified based on the natural shape of the aggregated particles such as granular, blocky, prismatic, columnar, or platy (derived from plate-like). Peds which have no internal structure or distinct shape are referred to as single grained or massive.[1]   
  • Soil texture refers to the relative proportion of the sizes of soil particles. It can be classified into sand, silt, and clay, ranging from the largest (0.05 to 2.0 mm) to the smallest (less than 2.0 microns).[2]  
  • Soil moisture or water content is the ratio of water mass to dry matter mass. 

These properties are determined by the ratio and composition of the forming components, hence each characteristic is interwoven and influences one another. For example, soil color is dependent on mineral species, composition, amount of organic matter, and moisture. 

Also, while minerals, ratio of minerals and organic matter, size of particles and pore space largely determine the soil structure and texture; these two latter properties affect the nutrient and water-holding ability, and the soil temperature, which ultimately affects its water content and biodiversity.[1,2]  

Types of Horizons

Horizons develop as layers from various soil-forming components. The newly added soil-forming materials are typically deposited on top of the older layer where they undergo various horizon development processes. In some cases, plants, soil-dwelling animals and weathering agents can move these materials to lower and older horizons. Similarly, weathering agents may remove soil-forming components from the developing soil profile.[1] Each horizon is typically designated by a specific letter to indicate its relative position in the soil profile and the observable characteristics. The following letters are typically used to designate horizons in the soil profile:[1]
  • O for organic horizon which is the soil-forming surface that consists mainly of decomposing organic matter.
    When dealing with the biological aspect, fresh litter such as dead plants and animals on top of the O horizon is sometimes separately designated as the L-layer. This is because the L-layer is newer and considerably more biologically active than O horizon.[2]
  • A horizon is the uppermost layer below the O horizon. This layer is characterized by a mixture of decomposed organic matter and mineral particles. These mineral particles are formed from weathering, gravitational movement, or accumulation of dirt particles – they can also be deposited from elsewhere.
  • E horizon refers to a bleached-color layer from loss of organic matter and minerals such as oxides of iron and aluminum.
  • B horizon is a dense layer where small soil-forming materials from the layers above are accumulated.  
  • C horizon represents the layer where the soil-forming materials are present – rocks are also present here.
Not every horizon is present in all soil profiles, thus each profile is unique. For example, a newly formed ground may contain only O-A-C horizons, whereas older ones may have four to five horizons.

Classification of Soil Biology (or Biota)

Most large animals that come in contact with the soil are typically restricted to its surface. Plants, small animals, and microorganisms, however, interact with the soil surface and exert their influence beyond the uppermost horizons. 

These organisms, which make up the soil biota or community, closely interact with the soil and play significant roles in developing soil profiles.[1]   

For instance, plants penetrate their roots into the ground as they grow. Microorganisms and animals such as ants, earthworms, millipedes, slugs, and shelled snails inhabit and feed on plant products and litter on the L-layer. 

Eventually, this L-layer becomes the O-horizon as the layer is being decomposed, while newer litter and organic matter are being formed on top of its surface. 

The several living organisms found underground can be classified based on their sizes:[2]

1. Macro- and megafauna

Macro- and megafauna are organisms whose body widths are larger than 2 mm and they consume dead plants and organic litter. Examples include moles, earthworms, ants, millipedes, beetles, termites, and scorpions.

2. Mesofauna

Mesofauna is a group of organisms whose body widths are between 0.1 mm to 2 mm. Microarthropods represent the most abundant and best-described mesofauna and act often as consumers. Examples are mites, springtails (Collembola), and pot worms. 

3. Microfauna

Microfauna refers to organisms whose body widths are less than 0.1 mm. Microfauna include:[2] 

  • Nematodes known as roundworms, which are free-living multicellular animals that typically live among ground particles. They act as primary consumers feeding on plant roots and litter from plants, or higher-level consumers feeding on bacteria, fungi, and other animals underground.     
  • Protozoa, a group of unicellular eukaryotes such as amoebae, ciliates, and flagellates. Some are capable of free-living while others are parasitic. Protozoa live in water-filled pore spaces and require water for movement. However, many protozoa form resistant structures called cysts to overcome drought conditions. They feed on bacteria, fungi, other protozoa, and small animals.

4. Microorganims

Microorganisms in soil communities are microbes such as bacteria, yeast, fungi, and algae. They represent the most abundant and diverse group of organisms, a few notable microbes are:[1]

  • Nitrogen fixers such as Azotobacter and Rhizobium. Azotobacter is a free-living bacteria, while Rhizobium colonizes the roots of legume plants to form a structure called root noodle. Both can fix nitrogen from the atmosphere and convert it to ammonium, increasing the nitrogen supply in the ground and providing the plants with their essential amino acids.
  • Nitrifiers are bacteria of the Nitrosomonas and Nitrobacter genera. They are capable of oxidizing ammonium to nitrate, i.e. nitrification, which facilitates the cycling of nitrogen from the ground back to the atmosphere. 
  • Mycorrhizae are fungi that colonize the cortical tissue of plant roots. In doing so, they acquire carbon sources from the plants, while delivering the colonizing plants with nutrients, especially phosphorus. The interaction between plants and mycorrhiza increases the plants’ fitness, allowing them to survive and thrive in harsh environments.

    Common mycorrhizal fungi are:[2]

    • Ectomycorrhizas or EM fungi, are frequently found in conifer roots grown in temperate forests.
    • Ericoid mycorrhizae are found in evergreen shrubs grown in the alpine and arctic tundra.
    • Arbuscular mycorrhizae are commonly found in the roots of various crops and legumes.  

The Importance of the Soil Biota

1. It contributes to the soil- and horizon-formation processes

These organisms influence soil-forming processes, development of horizons and soil profiles.  Their activities are regarded as biological weathering agents, which wear away rocks and decompose organic matter, leading to horizon development and formation.   For instance, 
  • Transformation describes a process of horizon development where the newly added soil-forming components are altered. Soil-forming components can be transformed by physical, chemical, and biological processes. 
    For example, when plants’ aboveground parts are shed on top of the surface of the ground, organisms consume these plant parts, breaking them into small pieces and decomposing them into organic matter. In the end, the organic matter accumulates and mixes with other soil-forming components to become another horizon in the soil profile.
  • Leaching is a pedogenic process in which soil-forming materials are translocated to lower horizons. The translocation of these components occurs with plant growth, microbial and animal activities.
    As plants grow, their roots penetrate the ground, causing soil-forming materials such as minerals and decomposed organic matter to move down the developing soil profile.
    Simultaneously, the movement of small animals and microorganisms as they feed on dead plants and litter also shifts dirt particles around and across the soil profile.   
In addition, animal and human interference can transport pedogenic components from one place to another or remove them from the developing soil profile, adding to the development of horizons and soil formation.

2. Soil biology provides nutrients and drives the nutrient cycle 

The biological activity of living organisms, especially microorganisms, provides the soil with nutrients and cycles them through the ecological food web of the site.

Food produced from plants grown aboveground is consumed by consumers that live in or below the ground. Wastes from food consumption, including plant, animal remains, and organic fertilizers, are decomposed, transforming them into nutrient forms that plants and other autotrophs can use to produce food

The nutrients are cycled through the food web when consumers feed on the food and defecate or die, and decomposers digest the feces or consumers’ remains into the form of nutrients that plants and autotrophs can use. 

Certain bacteria and fungi can enrich the soil with nutrients. Nitrogen fixers acquire nitrogen from the atmosphere, supplying it with ammonium while nitrifiers convert ammonium into nitrates. 

Mycorrhiza can provide phosphorus in exchange for carbon sources derived from the plants they colonize. These minerals can be assimilated by plants and other autotrophs to produce food for consumers.

3. Soil biota shapes soil properties and fertility

The ratio of soil-forming components determine its properties, including soil structure, texture, and moisture. To a certain degree, these properties are dictated by the biodiversity of the soil biota and their interactions with the soil.     

The rate of organic matter decomposition and nutrient release relies on the species present on the location. In other words, the number of organisms and the species that decompose and transform organic matter into consumable nutrients affect the ratio of organic matter, water content, and air space between the components.

The composition of the soil dictates its structure and texture, which, in turn, prescribes the compatibility of the site for organisms to inhabit. Ultimately, the inhabiting organisms condition the soil fertility by acquiring or making nutrients available for autotrophs’ use, determining the suitability of its applications.[1]


Soil serves as a platform for the growth and development of microbes, plants, and animals that live above, in or below ground. Their interaction with the soil and with one another is depicted in a soil profile, consisting of several layers called horizons. 

Overall, soil biology looks into the dynamics of the soil, in view of its occupying creatures and their impact on its properties and formation. Such understanding is useful in assessing its potential for use in agriculture and other human activities.


  1. Jhonson C, Biology of Soil Science. Jaipur: Oxford Book Company; 2009. 
  2. Bardgett R, The Biology of Soil: A Community and Ecosystem Approach. New York: Oxford University Press; 2005