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Annex 2
The soil ecosystem

"After two to three days without rains, the ground became very dry and even the weeds would not grow." Resource-poor farmer in El Salvador

The soil ecosystem can be defined as an interdependent life-support system composed of air, water, minerals, and macro- and micro-organisms. These organisms can in turn be distinguished into flora (for example plants and micro-flora such as algae, bacteria and fungi) and fauna (for example earthworms, millipedes, woodlice, slugs and snails, and micro-fauna such as protozoa and nematodes) (Brussaard and Juma, 1995). This soil biota, one of the most important components of the soil, plays a major role in many essential natural processes, which determine nutrient recycling and nutrient and water availability for agricultural productivity.

Box A1. Roles of the soil ecosystem

A healthy soil ecosystem will:

  • Decompose organic matter into humus;
  • Retain nitrogen and other plant nutrients;
  • Glue soil particles together and create pores for best passage of air and water;
  • Protect roots from diseases and parasites;
  • Make available nutrients to the plant;
  • Produce hormones that help plants grow;
  • Retain water.

The soil structure

The arrangement of the solid particles and spaces commonly referred to as soil structure is highly complex and dynamic. It depends on its components and their physical, chemical and biological interactions. Of special importance are soil texture (particle size distribution); chemical composition and charge distribution of minerals; organic components (humus, humic substances, organic acids etc.; the actions of roots, soil fauna and flora; the physical and chemical action of water; temperature; various forces of aggregation and disaggregation; etc.

Through these actions, soil components are mixed, aggregated or separated, and a complex of solid materials and pores is created where air, water and nutrients can circulate and be stored, and where roots, animals and micro-organisms develop.

Its present condition may be altered - all too often degraded - by inappropriate management, which results in compaction, pulverisation and interstitial sealing.

The physical arrangement of the spaces or pore is where most of the important changes take place: water movement, root extension and enlargement, gas exchange, particularly of oxygen and carbon dioxide in the processes of respiration by roots and micro-organisms. Therefore emphasis should be given on the spaces more than on the solid particles because of their critical relationship with soil moisture in soil-water-plant relationships and dynamics. The roles of organic matter, roots and soil fauna are most important in the development of pores, and thus for air, water and nutrients circulation.

Natural cycles: air, water, nutrients

Soil water

Water is critical to crop production in many areas, especially in Africa. There are arid or semi-arid areas in all continents, and even in areas with adequate average rainfall droughts or dry spells frequently occur.

The amount of rainwater that infiltrates depends on the nature of the soil surface and the capacity of the soil to retain and transport water. After infiltration, some of this water percolates downwards (and is eventually stored in the groundwater), some is absorbed by plants and released into the air, some evaporates from the soil surface, and the rest is stored as bound water.

Water in the soil is important for plants and soil life (water and nutrient supply) and for soil genesis (weathering, humus, movement of particles, etc.). Soil water is a vehicle for nutrients and is necessary for biological and chemical reactions in the soil, which build in particular the soil fertility.

Organic matter plays an important role in the water cycle as it facilitates infiltration and water storage, structure building for water circulation and production of colloids which retain water. Micro- and macro-organisms also play major role in creating pores and various forms of organic matter.

Soil air

Air is necessary for the respiration of soil fauna and flora, including plant roots. It also plays an important role in chemical reactions.

The composition of the soil air is different from that of the atmosphere. The respiration of roots and other organisms results in the CO2 content of soil air in the surface soil being about ten times that of the atmosphere (Schroeder, 1984). Exchanges between soil air and atmosphere (soil respiration) are through diffusion, depending on the CO2 and O2 pressures and the permeability of the soil (in turn affected by soil structure and water content).

In the soil, water and air use the same channels, the pores. Air and water share the same spaces; some air can be dissolved in soil water and some can also be stored in the larger pores not occupied by water, often those resulting from the activities of macrofauna or decay of roots.

Nutrient cycles

The main nutrient cycles (especially the nitrogen cycle) in the soil are linked with the activity and cycles of soil life, for example organic matter decomposition, production of organic acids, nitrogen fixation. The decomposition of the soil organic matter is called mineralisation and produces primarily simple forms of nutrients containing nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg) and sulphur (S). The weathering of soil minerals can also release K, Ca, Mg and iron (Fe). Carbon (C), which represents around 47 percent of the dry mass of organic matter, is released into the atmosphere through respiration. Water and energy are also produced during these processes.

A portion of the nutrients present in the soil may be found in the soil water, circulating and being taken up by plant roots and soil organisms. Some are lost through leaching or as gases (for example NH3); but an important part is stored on organic or mineral surfaces at anionic and cationic binding sites depending on soil properties (especially cation exchange capacity CEC), pH, concentrations in soil solution, etc. These nutrients can be released into the soil solution where the concentration or the pH diminish, for example adjacent to roots.

These nutrient exchanges between organic matter, water and soil affect soil fertility and need to be maintained, especially for production purposes. If the soil is exploited for crop production (export of nutrients) without restoring the organic matter and nutrient contents and keeping a good structure, the cycles are broken and soil fertility declines.

The organic matter

The decomposition process

Decomposition is the physical breakdown and biochemical transformation by saprophytic fungi and bacteria1 of complex organic molecules of dead material into simpler organic and inorganic molecules, which may be used again by other organisms (Juma, 1998). In general bacteria break down readily decomposable organic material, which results in nutrients such as especially N, P and S becoming available for uptake by other organisms. This process is called mineralisation2.

The waste products from bacteria become soil organic matter. This waste material is less decomposable than the original plant and animal material, but can be used by a large number of other organisms. Fungi break down the less decomposable organic matter and retain those nutrients in the soil as fungal biomass. Just like bacteria, fungal waste products become soil organic matter, and these waste materials are used by other organisms. Less resistant plant materials are broken down first, whereas the breakdown of more resistant materials, such as lignin and protein, takes place in several stages. The decomposition process can take part in aerobic or in anaerobic conditions.

Humus: composition and role

Subsequent decomposition of dead material and modified organic matter results in the formation of more complex organic matter, called humus (Juma, 1998). This process is called humification. Humus consists of a group of humic substances that includes humic acids, fulvic acids, hymatomelanic acids and humins (Tan, 1994) and is probably the most widely distributed organic carbon-containing material in terrestrial and aquatic environments.

One of the most striking characteristics of humic substances is their ability to interact with metal ions, oxides, hydroxides, minerals and organics, including toxic pollutants, to form water-soluble and water-insoluble associations. Through the formation of these complexes, humic substances can dissolve, mobilise and transport metals and organics in soils and waters, or bring about an accumulation in certain soil horizons. An example of the former is their effect on nutrient availability, especially those present at micro-concentrations only (Schnitzer, 1986); while an example of the latter is their ability to reduce the toxicity of, for instance aluminium in acid soils (Tan and Binger, 1986) or to capture pollutants such as herbicides (such as atrazine) or insecticides (such as tefluthrin) in the cavities of the humic substances (Vermeer, 1996).

Humic substances enhance plant growth directly through physiological and nutritional effects. Thus humic acid is capable of improving seed germination, root initiation and uptake of plant nutrients, and serves as a source of nitrogen, phosphorus and sulphur (Tan, 1994; Schnitzer, 1986). Indirectly, they may affect plant growth through modifications of physical, chemical and biological properties of the soil, such as an increase in water holding capacity and cation exchange capacity, and improvement of tilth and aeration through good soil structure (Stevenson, 1994).

The soil life

Predator-prey relationships: a source of nitrogen

As in all ecosystems, feeding relationships between organisms also exist in the soil. Energy is transferred from the primary producers (green plants) through a series of organisms that eat and are eaten, starting with bacteria and fungi, which feed on organic matter (primary consumers). The main effect of this soil activity is the release of nitrogen for plant growth.

Protozoa are one-celled, highly mobile organisms that feed on bacteria and on each other. Because protozoa require five to ten-fold less nitrogen than bacteria, N is released when a protozoan eats a bacterium. The released N is then available plant uptake. Between 40 and 80 percent of the N in plants can come from the predator-prey interaction of protozoa with bacteria.

Nematodes are tiny, worm-like, multicellular organisms, which live in the maze of interconnected pores in the soil. They move in the films of water that adhere to soil particles. Beneficial nematodes eat bacteria, fungi and other nematodes. Nematodes need even less nitrogen than protozoa, between 10 and 100 times less than the equivalent live mass of bacteria, or between 5 and 50 times less than the equivalent weight of fungal hyphae. Thus when nematodes eat bacteria or fungi, nitrogen is released and becomes available for plant growth.

Micro-arthropods have several functions. They chew plant leaf material, roots, stems and tree trunks into smaller pieces, making it easier for bacteria and fungi to find the food they like on the newly exposed surfaces. Arthropods can increase decomposition rates by two to 100 times, although if the bacteria and fungi are lacking, increased decomposition will not occur. In many cases however, the arthropods carry around an inoculum of bacteria and fungi, making certain the food they want is inoculated onto the newly exposed surfaces. The arthropods then feed on the bacteria and fungi and, because the C/N ratio of arthropods is many times higher than that of the bacteria and fungi, release nitrogen, which is then available for plant growth.

Earthworms: the soil managers

Large soil organisms such as earthworms mix plant material into the soil. Three groups of earthworms can be distinguished (Edwards and Lofty, 1977):

The burrowing activity of earthworms provides channels for air and water, which has an important effect on the oxygen diffusion in the root zone, and the drainage of water from it. The shallow-dwelling earthworms create numerous channels throughout the topsoil, which increases overall porosity. The large vertical channels created by the deep-burrowing earthworms greatly increase water infiltration under intense rainfall or ponding conditions. Earthworms can also aid extensive root growth in the subsoil, due to higher nitrogen availability in the casts (up to four times more total nitrogen than in the topsoil) and easier penetration into the soil through existing channels (Plate A2.1).

Plate A2.1

Earthworm casts contain up to four times more nitrogen than the surrounding soil, and earthworm burrowing activity improves water and air exchange within the soil

[A. Odoul/FAO/17749]

Plant-micro-organism interactions

Plant roots anchor the plant to the ground and absorb water and nutrients. They also create a distinct ecosystem that can profoundly alter plant growth. This often-neglected ecosystem is the rhizosphere, which is the outer part of the root and the area immediately adjacent to it.

A large number of micro-organisms congregate around the surfaces of plant roots. They are attracted to the root surface because of chemical compounds secreted by live roots, which are vital sources of food and energy for the micro-organisms. These root exudates can be distinguished into three groups (Jackson, 1993):

The microbes that inhabit the rhizosphere are a mixture of beneficial, neutral and harmful organisms. The majority of the micro-organisms are beneficial. The microbes in the rhizosphere extract nutrients and energy from the root and its products. In return, some of the products of the micro-organisms regulate plant growth. This regulation is affected by environmental factors (biological, chemical and physical) which, together with factors such as the species of the plant and its age etc., also affect the mix and concentration of micro-organisms surrounding a particular root.

Some examples of beneficial micro-organisms and their functions are Rhizobium and Mycorrhizae. The roots of leguminous plants can be infected by Rhizobium bacteria: when a root hair comes into contact with a bacterium, the root hair curls and the cell walls dissolve under influence of enzymes, thus forming a nodule (Plate A2.2). Once inside the nodule the bacterium obtains its necessary nutrients from the host plant and in turn the host plant receives nitrogen compounds produced by the bacteria from nitrogen gas in the soil atmosphere. An association with mutual benefits is called a symbiosis, hence the name symbiotic nitrogen fixation3.

Plate A2.2

Symbiotic bacteria, chiefly associated with leguminous plants and occurring in root nodules, enrich soils by adding nitrogen, a key plant nutrient. Nodules containing bacteria on the roots of a Vetch plant

[T.F. Shaxson]

Mycorrhizae are fungi that form a network of mycelia or threads on the roots and extend the surface area of the roots. They grow in the younger roots, as in mature roots the cortex is broken away. Fine roots are the primary sites of mycorrhizal development as they are the most active sites for nutrient uptake. The roots of most plants are infected with mycorrhizal fungi.

This symbiotic association between certain groups of soil fungi and plant roots enhances plant growth by enabling a greater proportion of the available nutrients and water in the soil to be absorbed by the plant. The benefits of effective association include protection against some root pathogens, increased disease tolerance, drought tolerance and protection against soil toxicity and high temperatures. There are several mechanisms of protection through Mycorrhizae (Linderman, 1994):

Like other fungi, Mycorrhizae also improve the soil structure by binding soil particles into more stable aggregates with mycorrhizal hyphae. The hyphae bind individual clay particles into aggregates, thereby allowing more oxygen to reach the root zone. This promotes the rapid multiplication of beneficial aerobic bacteria, which may fix nitrogen, solubilize phosphorus, and process other elements into forms that plants can use. As the fungi are also aerobic organisms, this forming of clay soil into a granular structure will also improve their own oxygen supply. The fungal hyphae will also bind together sand, which then becomes a better moisture-holding environment for plant roots and bacteria.

Mycorrhizae can form a hyphae-linked underground network to "borrow" nutrients from older trees to feed young seedlings.

Plant-parasitic organisms

In contrast to the beneficial soil micro-organisms, other soil micro-organisms are pathogenic to plants and may cause considerable damage to crops. Large numbers of pathogenic micro-organisms are normally present in the soil and many of them can infect plant roots. However, certain micro-organisms present in the soil are antagonistic to these pathogens and can prevent the infection, as in case of the Myccorhizae.

Plant-parasitic nematodes are found in association with most plants. Some are endoparasitic: living and feeding within plant tissue, while others are ectoparasitic: feeding externally through plant walls. The former can kill or reduce plant productivity, while the latter can provide an entry point for disease-causing fungi and bacteria. Root-feeding nematodes are very opportunistic and are among the first organisms to invade a volume of soil.


Brussaard, L. and Juma, N.G. 1995. Organisms and humus in soils. In: A. Piccolo (Ed.) Humic substances in terrestrial ecosystems. Elsevier. Amsterdam. pp.329-359.

Edwards, C.A. and Lofty, J.R. 1977: Biology of Earthworms. Chapman and Hall. 333p.

Jackson, W.R. 1993. Humic, fulvic and microbial balance: organic soil conditioning. Jackson Research Center. 946p.

Juma, N.G. 1998.The pedosphere and its dynamics: a systems approach to soil science. Volume 1. Quality Color Press Inc. Edmonton, Canada. 315p.

Linderman, R. G. 1994. General summary. In: Mycorrhizae and Plant Health. F. L. Pfleger and R. G. Linderman (Eds.), APS Press, St. Paul. pp.1-26.

Schnitzer, M. 1986. The synthesis, chemical structure, reactions and functions of humic substances. In: Humic substances: effect on soil and plants. R.G. Burns, G. dell' Agnola, S. Miele, S. Nardi, G. Savoini, M. Schnitzer, P. Sequi, D. Vaughan and S.A. Visser (Eds.) Congress on Humic Substances. March 1986, Milan.

Stevenson, F.J. 1994. Humus Chemistry. Genesis, Composition, Reactions. Wiley Interscience. New York 2nd Edition. 512p.

Tan, K.H. 1994. Environmental soil science. Marcel Dekker Inc. New York. 304 p.

Tan, K.H. and Binger, A. 1986. Effect of humic acid on aluminium toxicity in corn plants. Soil Science 14: 20-25.

Vermeer, A.W.P. 1996. Interactions between humic acid and hematite and their effects on metal ion speciation. PhD. Thesis. Wageningen University.

11 Organic C +O2 à microbial biomass + CO2

2 Organic N à NH4+ à Nitrosomonas àNO2- à Nitrobacter à NO3-

3 Symbiotic nitrogen fixation: N2 (atmosphere) à Rhizobium à N organic (soil)

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