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Horticulture 1000
HT1032 - Soils 2 - Soil organisms
Amount of organic matter in soil Physical properties

Soil organisms

There are many  different plants and animals that live in the soil. They mostly live in the  topsoil. Topsoil is warm and moist and there is oxygen and food.

The living  organisms and animals in the soil have an important job in the natural cycling  of organic matter, the release of nutrients and the formation of humus.

Some  of the larger common soil organisms

Here are some  of the larger common soil organisms.

Most of the  important soil organisms are much smaller than those shown, and you need a  microscope to see them in any detail.


These are  microscopic, single-celled organisms. They like warm, moist soils of neutral  pH. They cannot make their own food so rely on ready-made sources of organic  material. Bacteria break down or decompose organic matter, and release  nutrients into the soil. They are called decomposers. They are needed to  decompose dead organic matter, droppings, and urine. Without them no soil could  maintain its fertility. An infertile or sandy soil has few bacteria.

There may be  1000 million bacteria in each gram of fertile soil. A hectare of soil can carry  up to one tonne of bacteria.

The nitrogen cycle

  • Nitrogen-fixing  bacteria in the soil take nitrogen from the air and fix it into nitrates.
  • These nitrates  get into the plant when it takes in water via its roots. The soluble nitrogen  will be absorbed from the soil water by plants, and used for growth.
  • Plants use  these nitrates to make proteins and grow.
  • When plants  decompose, one of the products released is ammonia. Special nitrifying bacteria  change this into nitrates, which can be used for new plant growth. This process  is called nitrification.
The nitrogen cycle

Denitrifying  bacteria that live in soils lacking in oxygen break down some of the soluble  nitrogen into nitrogen gas. They do this to make use of the oxygen released.  The nitrogen then goes back into the atmosphere where it is once again unavailable  for plants to use. This process is called denitrification. Nitrogen can also be lost by  leaching.

Legume plants and nitrogen fixation

Legumes are  plants in the pea family. They can add nitrogen to the soil and turn  atmospheric nitrogen into a form that plants can use.

Root nodules on a clover plant

They do this  with the help of bacteria that live in nodules in their roots. The bacteria  belong to the genus Rhizobia (say rye-zo-bee-a). Rhizobia bacteria invade plant  roots through the root hairs. Together, the plant cells and the bacteria form  structures on the roots called nodules.


The majority of  fungi in soil feed on dead organic matter. Their main role is decomposition of  organic matter. Fungi are important because many can rot cellulose and lignin.  These are the plant compounds that most animals find impossible to digest.  Fungi, along with bacteria, break them down into simpler compounds that plants  can absorb as nutrients.

Some fungi live in associations with plant roots. The  fungal threads grow among and often into the plant roots. They gain shelter and  carbohydrates from the plant.

In return the plant absorbs water and nutrients from the soil at a greater rate than if the fungus was not present.


Earthworms feed on dead organic matter such as leaves. They drag this material down into their burrows where they feed on it. Later they return to the surface and deposit any undigested material plus soil they have swallowed as worm casts.

This habit of dragging organic matter down into burrows and depositing casts on the surface turns soil and mixes organic matter into soil. Earthworms rapidly improve the  soil structure.

Soil pests

Many of the organisms that are important in nutrient cycling and the breakdown of organic matter can also be pests in the soil.

Many plant pests are arthropods. These are joint-legged animals, with external skeletons and a body made up of several different parts. Insects, crustacean, spiders and woodlice are all arthropods.

The table below tells you where the most common soil arthropods live and how they damage plants.

woodlice damp organic soils eat roots and lower leaves
millipedes most soils occasionally eat underground tubers and seeds
mites soils and plant tissues mottle or distort leaves, buds, flowers and bulbs
springtails soil and decaying humus eat fine roots
beetles mainly in soil eat roots and succulent tubers
earwigs flowers and soil eat flowers
Grass grub

The grass grub feeds on grass roots, which prevents growth.


They break down  organic matter in soil, but some are serious plant pests. Nematodes attack the  roots and plant tissue. They attack plants such as potato, onions, beans, bulbs  and strawberries.

Nematodes are difficult to control because they  produce a large number of eggs, and the cysts can survive in soil for 10 years  or more in some species.

Bacteria, fungi and viruses

Some specific  types of bacteria and fungi in the soil cause disease. All viruses cause  diseases or disorders.


Some soil  bacteria are pathogens. Pathogens are disease-causing organisms. Galls and root  rots are examples. They cause plant roots to rot and then the plant will  collapse and die.


Fungi can grow  rapidly in plant tissues when conditions suit them. Some soil fungi can cause  diseases. They cause plants to rot.

  • Damping off is  a disease that can affect all seedlings.
  • Verticillum  wilt causes damage to the roots of a plant and then it will wilt and die.
  • Phytophthora is  a soil-borne disease that causes damage to the roots.
This brassica has clubroot

This brassica has clubroot.

Clubroot is a disease that affects brassica plants. It is caused by a fungus in the soil that makes the roots become very thick and swollen. The roots are unable to take up enough water and nutrients. This causes the plants to have stunted growth.


There are a number  of ways viruses can be transferred through the soil.

  • Infected roots  can spread them to other roots.
  • Infected  cuttings, bulbs, corms and tubers can establish the disease in new plants.
  • A few viruses  survive in the soil or carry over in roots and stalks from the previous season.  Tobacco mosaic virus is an example, which infects tomatoes. It causes a mosaic  or mottled effect on leaves, and stunting and distortion.

Soil sterilisation

Soil sterilisation is used to control soil pests and diseases. Steam treatment involves using high-pressure steam to kill the pests. Chemical treatment uses substances which are toxic to most living organisms.

Complete Activity 5A in the workbook

Key points   Key points

  • Soil contains a  wide range of living organisms that are vital for nutrient cycling.
  • Most soil  organisms prefer loamy soils that are slightly acidic, with plenty of organic  matter and are moist. Bacteria are found in large numbers in most soils. They  help provide nitrates for plant growth and are essential for the decomposition  process.
  • Fungi are  important both in association with plant roots and as decomposers of cellulose  and lignin.
  • Earthworms help  bring organic matter into soil and begin the breakdown process. They help to  distribute the organic matter throughout the topsoil.
        Many other  small organisms are active in the soil, breaking organic matter down to simpler  particles.
  • Some soil  organisms can be pests. Nematodes are a major soil pest of plant crops. They  cause much damage and are difficult to control.
  • Bacteria, fungi  and viruses are all found in soil and many can cause diseases in crops.
  • Soil sterilisation is used  to control many soil pests and diseases.

What's next?

Go to: 6 Physical properties.

Amount of organic matter in soil Physical properties