Soil Ecosystems: The Soil Food Web

Module Progress:

After exploring the global processes involved with soil building and management, this module takes the same ecosystem approach you’ve been using and applies it to the soil. In this way, you can understand what we really mean when we say that soil is “alive”, and start to imagine ways that different types of agricultural has various impacts on the soil ecosystem.

Excerpt 1: The importance of Soil Organic Matter – Key to Drought Resistant Soil and Sustained Food and Production

Chapter 2 from the FAO Soils Bulletin

When plant residues are returned to the soil, various organic compounds undergo decomposition. Decomposition is a biological process that includes the physical breakdown and biochemical transformation of complex organic molecules of dead material into simpler organic and inorganic molecules (Juma, 1998). The continual addition of decaying plant residues to the soil surface contributes to the biological activity and the carbon cycling process in the soil. Breakdown of soil organic matter and root growth and decay also contribute to these processes. Carbon cycling is the continuous transformation of organic and inorganic carbon compounds by plants and micro- and macro-organisms between the soil, plants and the atmosphere.

Decomposition of organic matter is largely a biological process that occurs naturally. Its speed is determined by three major factors: soil organisms, the physical environment and the quality of the organic matter (Brussaard, 1994). In the decomposition process, different products are released: carbon dioxide (CO2), energy, water, plant nutrients and resynthesized organic carbon compounds. Successive decomposition of dead material and modified organic matter results in the formation of a more complex organic matter called humus (Juma, 1998). This process is called humification. Humus affects soil properties. As it slowly decomposes, it colours the soil darker; increases soil aggregation and aggregate stability; increases the CEC (the ability to attract and retain nutrients); and contributes N, P and other nutrients.Important discoveries about soil have occurred since Liebig’s time. In 1870, Louis Pasteur, for whom pasteurization is named, suggested that ammonium was converted into its plant-usable form, nitrate, through the active mediation of soil bacteria. Since then, the value of soil ecology has increased.

Soil organisms, including micro-organisms, use soil organic matter as food. As they break down the organic matter, any excess nutrients (N, P and S) are released into the soil in forms that plants can use. This release process is called mineralization. The waste products produced by micro-organisms are also soil organic matter. This waste material is less decomposable than the original plant and animal material, but it can be used by a large number of organisms. By breaking down carbon structures and rebuilding new ones or storing the C into their own biomass, soil biota plays the most important role in nutrient cycling processes and, thus, in the ability of a soil to provide the crop with sufficient nutrients to harvest a healthy product. The organic matter content, especially the more stable humus, increases the capacity to store water and store (sequester) C from the atmosphere.

The Soil Food Web

The soil ecosystem (Box 1) can be defined as an interdependent life-support system composed of air, water, minerals, organic matter, and macro- and micro-organisms, all of which function together and interact closely.

The organisms and their interactions enhance many soil ecosystem functions and make up the soil food web. The energy needed for all food webs is generated by primary producers: the plants, lichens, moss, photosynthetic bacteria and algae that use sunlight to transform CO2 from the atmosphere into carbohydrates. Most other organisms depend on the primary producers for their energy and nutrients; they are called consumers.


Some functions of a healthy soil ecosystem

  • Decompose organic matter towards humus.
  • Retain N and other nutrients.
  • Glue soil particles together for best structure.
  • Protect roots from diseases and parasites.
  • Make retained nutrients available to the plant.
  • Produce hormones that help plants grow.
  • Retain water.

Soil life plays a major role in many natural processes that determine nutrient and water availability for agricultural productivity. The primary activities of all living organisms are growing and reproducing. By-products from growing roots and plant residues feed soil organisms. In turn, soil organisms support plant health as they decompose organic matter, cycle nutrients, enhance soil structure and control the populations of soil organisms, both beneficial and harmful (pests and pathogens) in terms of crop productivity.

The living part of soil organic matter includes a wide variety of micro-organisms such as bacteria, viruses, fungi, protozoa and algae. It also includes plant roots, insects, earthworms, and larger animals such as moles, mice and rabbits that spend part of their life in the soil. The living portion represents about 5 percent of the total soil organic matter. Micro-organisms, earthworms and insects help break down crop residues and manures by ingesting them and mixing them with the minerals in the soil, and in the process recycling energy and plant nutrients. Sticky substances on the skin of earthworms and those produced by fungi and bacteria help bind particles together. Earthworm casts are also more strongly aggregated (bound together) than the surrounding soil as a result of the mixing of organic matter and soil mineral material, as well as the intestinal mucus of the worm. Thus, the living part of the soil is responsible for keeping air and water available, providing plant nutrients, breaking down pollutants and maintaining the soil structure.

The composition of soil organisms depends on the food source (which in turn is season dependent). Therefore, the organisms are neither uniformly distributed through the soil nor uniformly present all year. However, in some cases their biogenic structures remain. Each species and group exists where it can find appropriate food supply, space, nutrients and moisture (Plate 2). Organisms occur wherever organic matter occurs (Ingham, 2000). Therefore, soil organisms are concentrated: around roots, in litter, on humus, on the surface of soil aggregates and in spaces between aggregates. For this reason, they are most prevalent in forested areas and cropping systems that leave a lot of biomass on the surface.

The activity of soil organisms follows seasonal as well as daily patterns. Not all organisms are active at the same time. Most are barely active or even dormant. Availability of food is an important factor that influences the level of activity of soil organisms and thus is related to land use and management (Figure 3). Practices that increase numbers and activity of soil organisms include: no tillage or minimal tillage; and the maintenance of plant and annual residues that reduce disturbance of soil organisms and their habitat and provide a food supply.

Different groups of organisms can be distinguished in the soil (Brussaard and Juma, 1995). Table 1 classifies them by size. Table 2 classifies them by function.

Table 1: Classification of soil organisms

Micro-organisms Microflora <5 µm



Microfauna <100 µm



Macro-organisms Meso-organisms 100 µm – 2 mm



Macro-organisms 2 – 20 mm




Snails and slugs

Plants Algae 10 µm
Roots > 10 µm

Note: Clay particles are smaller than 2 µm.

Table 1. Classification of soil organisms. Table from Swift, Heal and Anderson, 1979.

Table 2: Essential functions performed by different members of soil organisms (biota)

Functions Organisms involved
Maintenance of soil structure Bioturbating invertebrates and plant roots, mycorrhizae and some other micro-organisms
Regulation of soil hydrological processes Most bioturbating invertebrates and plant roots
Gas exchange and carbon sequestration (accumulation in soil) Mostly micro-organisms and plant roots, some C protected in large compact biogenic invertebrate aggregates
Soil detoxification Mostly micro-organisms
Nutrient cycling Mostly micro-organisms and plant roots, some soil- and litter-feeding invertebrates
Decomposition of organic matter Various saprophytic and litter-feeding invertebrates (detritivores), fungi, bacteria, actinomycetes and other micro-organisms
Suppression of pests, parasites and diseases Plants, mycorrhizae and other fungi, nematodes, bacteria and various other micro-organisms, collembola, earthworms, various predators
Sources of food and medicines Plant roots, various insects (crickets, beetle larvae, ants, termites), earthworms, vertebrates, micro-organisms and their by-products
Symbiotic and asymbiotic relationships with plants and their roots Rhizobia, mycorrhizae, actinomycetes, diazotrophic bacteria and various other rhizosphere micro-organisms, ants
Plant growth control (positive and negative) Direct effects: plant roots, rhizobia, mycorrhizae, actinomycetes, pathogens, phytoparasitic nematodes, rhizophagous insects, plant-growth promoting rhizosphere micro-organisms, biocontrol agents Indirect effects: most soil biota

Soil microorganisms have different functions in the soil food web. Soil biota can be grouped according to the function provided by the organism to the ecosystem, and the ecosystem functions can be related to the goods and services that come from the ecosystem. The chart above shows these relationships.


Chart 1: The Soil Food Web

Chart 1. The Soil Food Web. Chart from Alexandra Bot and José Benites, FAO Land and Plant Nutrition Management Service, Rome: FAO. 2005.